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1.
J Biol Chem ; 300(3): 105755, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38364890

RESUMO

XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal tail. It carries a putative phospholipid translocation path of multiple hydrophobic and charged residues in the transmembrane region. It also has a crucial tryptophan at the exoplasmic end of the path that regulates its scrambling activity. We herein investigated the tertiary structure of the human XKR8-basigin complex embedded in lipid nanodiscs at an overall resolution of 3.66 Å. We found that the C-terminal tail engaged in intricate polar and van der Waals interactions with a groove at the cytoplasmic surface of XKR8. These interactions maintained the inactive state of XKR8. Point mutations to disrupt these interactions strongly enhanced the scrambling activity of XKR8, suggesting that the activation of XKR8 is mediated by releasing the C-terminal tail from the cytoplasmic groove. We speculate that the cytoplasmic tail region of XKR8 functions as a plug to prevent the scrambling of phospholipids.


Assuntos
Proteínas Reguladoras de Apoptose , Basigina , Proteínas de Membrana , Proteínas de Transferência de Fosfolipídeos , Humanos , Proteínas Reguladoras de Apoptose/química , Proteínas Reguladoras de Apoptose/genética , Basigina/química , Membrana Celular/metabolismo , Lipossomos/química , Proteínas de Membrana/química , Proteínas de Membrana/genética , Nanopartículas/química , Proteínas de Transferência de Fosfolipídeos/química , Proteínas de Transferência de Fosfolipídeos/genética , Fosfolipídeos , Conformação Proteica em alfa-Hélice , Imagem Individual de Molécula
2.
Proc Natl Acad Sci U S A ; 119(15): e2123226119, 2022 04 12.
Artigo em Inglês | MEDLINE | ID: mdl-35380894

RESUMO

Cryoelectron microscopy (cryo-EM) was applied to Na+,K+-ATPase (NKA) to determine the structures of two E2P states, one (E2PATP) formed by ATP and Mg2+ in the forward reaction, and the other (E2PPi) formed by inorganic phosphate (Pi) and Mg2+ in the backward reaction, with and without ouabain or istaroxime, representatives of classical and new-generation cardiotonic steroids (CTSs). These two E2P states exhibit different biochemical properties. In particular, K+-sensitive acceleration of the dephosphorylation reaction is not observed with E2PPi, attributed to the presence of a Mg2+ ion in the transmembrane cation binding sites. The cryo-EM structures of NKA demonstrate that the two E2P structures are nearly identical but Mg2+ in the transmembrane binding cavity is identified only in E2PPi, corroborating the idea that it should be denoted as E2PPi·Mg2+. We can now explain why the absence of transmembrane Mg2+ in E2PATP confers the K+ sensitivity in dephosphorylation. In addition, we show that ATP bridges the actuator (A) and nucleotide binding (N) domains, stabilizing the E2PATP state; CTS binding causes hardly any changes in the structure of NKA, both in E2PATP and E2PPi·Mg2+, indicating that the binding mechanism is conformational selection; and istaroxime binds to NKA, extending its aminoalkyloxime group deep into the cation binding site. This orientation is upside down compared to that of classical CTSs with respect to the steroid ring. Notably, mobile parts of NKA are resolved substantially better in the electron microscopy (EM) maps than in previous X-ray structures, including sugars sticking out from the ß-subunit and many phospholipid molecules.


Assuntos
Glicosídeos Cardíacos , Cardiotônicos , Etiocolanolona/análogos & derivados , Ouabaína , ATPase Trocadora de Sódio-Potássio , Trifosfato de Adenosina/metabolismo , Glicosídeos Cardíacos/farmacologia , Cardiotônicos/farmacologia , Cátions/química , Cátions/metabolismo , Microscopia Crioeletrônica , Etiocolanolona/farmacologia , Magnésio/química , Magnésio/metabolismo , Ouabaína/farmacologia , Domínios Proteicos , Sódio/química , Sódio/metabolismo , ATPase Trocadora de Sódio-Potássio/química , ATPase Trocadora de Sódio-Potássio/metabolismo
3.
Proc Natl Acad Sci U S A ; 119(33): e2208004119, 2022 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-35939705

RESUMO

The cohesin complex is required for sister chromatid cohesion and genome compaction. Cohesin coiled coils (CCs) can fold at break sites near midpoints to bring head and hinge domains, located at opposite ends of coiled coils, into proximity. Whether ATPase activities in the head play a role in this conformational change is yet to be known. Here, we dissected functions of cohesin ATPase activities in cohesin dynamics in Schizosaccharomyces pombe. Isolation and characterization of cohesin ATPase temperature-sensitive (ts) mutants indicate that both ATPase domains are required for proper chromosome segregation. Unbiased screening of spontaneous suppressor mutations rescuing the temperature lethality of cohesin ATPase mutants identified several suppressor hotspots in cohesin that located outside of ATPase domains. Then, we performed comprehensive saturation mutagenesis targeted to these suppressor hotspots. Large numbers of the identified suppressor mutations indicated several different ways to compensate for the ATPase mutants: 1) Substitutions to amino acids with smaller side chains in coiled coils at break sites around midpoints may enable folding and extension of coiled coils more easily; 2) substitutions to arginine in the DNA binding region of the head may enhance DNA binding; or 3) substitutions to hydrophobic amino acids in coiled coils, connecting the head and interacting with other subunits, may alter conformation of coiled coils close to the head. These results reflect serial structural changes in cohesin driven by its ATPase activities potentially for packaging DNAs.


Assuntos
Adenosina Trifosfatases , Proteínas de Ciclo Celular , Proteínas Cromossômicas não Histona , Segregação de Cromossomos , Schizosaccharomyces , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Substituição de Aminoácidos , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Proteínas Cromossômicas não Histona/genética , Proteínas Cromossômicas não Histona/metabolismo , DNA/metabolismo , Mutação , Domínios Proteicos , Schizosaccharomyces/enzimologia , Schizosaccharomyces/genética , Proteínas de Schizosaccharomyces pombe/genética , Coesinas
4.
Proc Natl Acad Sci U S A ; 118(1)2021 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-33318128

RESUMO

The sodium pump (Na+, K+-ATPase, NKA) is vital for animal cells, as it actively maintains Na+ and K+ electrochemical gradients across the cell membrane. It is a target of cardiotonic steroids (CTSs) such as ouabain and digoxin. As CTSs are almost unique strong inhibitors specific to NKA, a wide range of derivatives has been developed for potential therapeutic use. Several crystal structures have been published for NKA-CTS complexes, but they fail to explain the largely different inhibitory properties of the various CTSs. For instance, although CTSs are thought to inhibit ATPase activity by binding to NKA in the E2P state, we do not know if large conformational changes accompany binding, as no crystal structure is available for the E2P state free of CTS. Here, we describe crystal structures of the BeF3- complex of NKA representing the E2P ground state and then eight crystal structures of seven CTSs, including rostafuroxin and istaroxime, two new members under clinical trials, in complex with NKA in the E2P state. The conformations of NKA are virtually identical in all complexes with and without CTSs, showing that CTSs bind to a preformed cavity in NKA. By comparing the inhibitory potency of the CTSs measured under four different conditions, we elucidate how different structural features of the CTSs result in different inhibitory properties. The crystal structures also explain K+-antagonism and suggest a route to isoform specific CTSs.


Assuntos
Glicosídeos Cardíacos/química , Glicosídeos Cardíacos/farmacologia , ATPase Trocadora de Sódio-Potássio/antagonistas & inibidores , ATPase Trocadora de Sódio-Potássio/química , Sódio/química , Animais , Fenômenos Biofísicos , Digoxina/farmacologia , Modelos Moleculares , Conformação Molecular , Ouabaína/farmacologia , Isoformas de Proteínas , Sódio/metabolismo , ATPase Trocadora de Sódio-Potássio/metabolismo
5.
Proc Natl Acad Sci U S A ; 115(21): E4833-E4842, 2018 05 22.
Artigo em Inglês | MEDLINE | ID: mdl-29735656

RESUMO

Cohesin is a fundamental protein complex that holds sister chromatids together. Separase protease cleaves a cohesin subunit Rad21/SCC1, causing the release of cohesin from DNA to allow chromosome segregation. To understand the functional organization of cohesin, we employed next-generation whole-genome sequencing and identified numerous extragenic suppressors that overcome either inactive separase/Cut1 or defective cohesin in the fission yeast Schizosaccharomyces pombe Unexpectedly, Cut1 is dispensable if suppressor mutations cause disorders of interfaces among essential cohesin subunits Psm1/SMC1, Psm3/SMC3, Rad21/SCC1, and Mis4/SCC2, the crystal structures of which suggest physical and functional impairment at the interfaces of Psm1/3 hinge, Psm1 head-Rad21, or Psm3 coiled coil-Rad21. Molecular-dynamics analysis indicates that the intermolecular ß-sheets in the cohesin hinge of cut1 suppressor mutants remain intact, but a large mobility change occurs at the coiled coil bound to the hinge. In contrast, suppressors of rad21-K1 occur in either the head ATPase domains or the Psm3 coiled coil that interacts with Rad21. Suppressors of mis4-G1326E reside in the head of Psm3/1 or the intragenic domain of Mis4. These may restore the binding of cohesin to DNA. Evidence is provided that the head and hinge of SMC subunits are proximal, and that they coordinate to form arched coils that can hold or release DNA by altering the angles made by the arched coiled coils. By combining molecular modeling with suppressor sequence analysis, we propose a cohesin structure designated the "hold-and-release" model, which may be considered as an alternative to the prevailing "ring" model.


Assuntos
Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/metabolismo , Proteínas Cromossômicas não Histona/química , Proteínas Cromossômicas não Histona/metabolismo , DNA Fúngico/metabolismo , Mutação , Proteínas Nucleares/metabolismo , Fosfoproteínas/metabolismo , Proteínas de Schizosaccharomyces pombe/química , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/genética , Proteínas de Ciclo Celular/genética , Cromátides/fisiologia , Proteínas Cromossômicas não Histona/genética , Segregação de Cromossomos , DNA Fúngico/genética , Modelos Moleculares , Proteínas Nucleares/genética , Fosfoproteínas/genética , Fosforilação , Conformação Proteica , Subunidades Proteicas , Schizosaccharomyces/crescimento & desenvolvimento , Schizosaccharomyces/metabolismo , Proteínas de Schizosaccharomyces pombe/genética , Supressão Genética , Coesinas
6.
Nature ; 502(7470): 201-6, 2013 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-24089211

RESUMO

Na(+),K(+)-ATPase pumps three Na(+) ions out of cells in exchange for two K(+) taken up from the extracellular medium per ATP molecule hydrolysed, thereby establishing Na(+) and K(+) gradients across the membrane in all animal cells. These ion gradients are used in many fundamental processes, notably excitation of nerve cells. Here we describe 2.8 Å-resolution crystal structures of this ATPase from pig kidney with bound Na(+), ADP and aluminium fluoride, a stable phosphate analogue, with and without oligomycin that promotes Na(+) occlusion. These crystal structures represent a transition state preceding the phosphorylated intermediate (E1P) in which three Na(+) ions are occluded. Details of the Na(+)-binding sites show how this ATPase functions as a Na(+)-specific pump, rejecting K(+) and Ca(2+), even though its affinity for Na(+) is low (millimolar dissociation constant). A mechanism for sequential, cooperative Na(+) binding can now be formulated in atomic detail.


Assuntos
Modelos Moleculares , ATPase Trocadora de Sódio-Potássio/química , Sódio/química , Animais , Sítios de Ligação , Cristalografia por Raios X , Rim/enzimologia , Estrutura Terciária de Proteína , Suínos
7.
Proc Natl Acad Sci U S A ; 110(17): 6805-10, 2013 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-23569276

RESUMO

Pestiviruses, including bovine viral diarrhea virus, are important animal pathogens and are closely related to hepatitis C virus, which remains a major global health threat. They have an outer lipid envelope bearing two glycoproteins, E1 and E2, required for cell entry. They deliver their genome into the host cell cytoplasm by fusion of their envelope with a cellular membrane. The crystal structure of bovine viral diarrhea virus E2 reveals a unique protein architecture consisting of two Ig-like domains followed by an elongated ß-stranded domain with a new fold. E2 forms end-to-end homodimers with a conserved C-terminal motif rich in aromatic residues at the contact. A disulfide bond across the interface explains the acid resistance of pestiviruses and their requirement for a redox activation step to initiate fusion. From the structure of E2, we propose alternative possible membrane fusion mechanisms. We expect the pestivirus fusion apparatus to be conserved in hepatitis C virus.


Assuntos
Vírus da Diarreia Viral Bovina Tipo 1/genética , Modelos Moleculares , Conformação Proteica , Proteínas do Envelope Viral/química , Sequência de Aminoácidos , Cristalografia por Raios X , Mapeamento de Epitopos , Dados de Sequência Molecular , Proteínas do Envelope Viral/genética , Internalização do Vírus
8.
J Biol Chem ; 288(9): 6602-16, 2013 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-23341448

RESUMO

The Na,K-ATPase is specifically inhibited by cardiotonic steroids (CTSs) like digoxin and is of significant therapeutic value in the treatment of congestive heart failure and arrhythmia. Recently, new interest has arisen in developing Na,K-ATPase inhibitors as anticancer agents. In the present study, we compare the potency and rate of inhibition as well as the reactivation of enzyme activity following inhibition by various cardiac glycosides and their aglycones at different pH values using shark Na,K-ATPase stabilized in the E2MgPi or in the E2BeFx conformations. The effects of the number and nature of various sugar residues as well as changes in the positions of hydroxyl groups on the ß-side of the steroid core of cardiotonic steroids were investigated by comparing various cardiac glycoside compounds like ouabain, digoxin, digitoxin, and gitoxin with their aglycones. The results confirm our previous hypothesis that CTS binds primarily to the E2-P ground state through an extracellular access channel and that binding of extracellular Na(+) ions to K(+) binding sites relieved the CTS inhibition. This reactivation depended on the presence or absence of the sugar moiety on the CTS, and a single sugar is enough to impede reactivation. Finally, increasing the number of hydroxyl groups of the steroid was sterically unfavorable and was found to decrease the inhibitory potency and to confer high pH sensitivity, depending on their position on the steroid ß-face. The results are discussed with reference to the recent crystal structures of Na,K-ATPase in the unbound and ouabain-bound states.


Assuntos
Glicosídeos Cardíacos/química , Inibidores Enzimáticos/química , Proteínas de Peixes/antagonistas & inibidores , Proteínas de Peixes/química , ATPase Trocadora de Sódio-Potássio/antagonistas & inibidores , ATPase Trocadora de Sódio-Potássio/química , Squalus acanthias , Animais , Estabilidade Enzimática/efeitos dos fármacos , Proteínas de Peixes/metabolismo , Concentração de Íons de Hidrogênio , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , ATPase Trocadora de Sódio-Potássio/metabolismo
9.
J Biol Chem ; 288(14): 10073-10081, 2013 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-23430748

RESUMO

Membrane proteins interact with phospholipids either via an annular layer surrounding the transmembrane segments or by specific lipid-protein interactions. Although specifically bound phospholipids are observed in many crystal structures of membrane proteins, their roles are not well understood. Na,K-ATPase is highly dependent on acid phospholipids, especially phosphatidylserine, and previous work on purified detergent-soluble recombinant Na,K-ATPase showed that phosphatidylserine stabilizes and specifically interacts with the protein. Most recently the phosphatidylserine binding site has been located between transmembrane segments of αTM8-10 and the FXYD protein. This paper describes stimulation of Na,K-ATPase activity of the purified human α1ß1 or α1ß1FXYD1 complexes by neutral phospholipids, phosphatidylcholine, or phosphatidylethanolamine. In the presence of phosphatidylserine, soy phosphatidylcholine increases the Na,K-ATPase turnover rate from 5483 ± 144 to 7552 ± 105 (p < 0.0001). Analysis of α1ß1FXYD1 complexes prepared with native or synthetic phospholipids shows that the stimulatory effect is structurally selective for neutral phospholipids with polyunsaturated fatty acyl chains, especially dilinoleoyl phosphatidylcholine or phosphatidylethanolamine. By contrast to phosphatidylserine, phosphatidylcholine or phosphatidylethanolamine destabilizes the Na,K-ATPase. Structural selectivity for stimulation of Na,K-ATPase activity and destabilization by neutral phospholipids distinguish these effects from the stabilizing effects of phosphatidylserine and imply that the phospholipids bind at distinct sites. A re-examination of electron densities of shark Na,K-ATPase is consistent with two bound phospholipids located between transmembrane segments αTM8-10 and TMFXYD (site A) and between TM2, -4, -6, -and 9 (site B). Comparison of the phospholipid binding pockets in E2 and E1 conformations suggests a possible mechanism of stimulation of Na,K-ATPase activity by the neutral phospholipid.


Assuntos
Regulação Enzimológica da Expressão Gênica , Lipídeos/química , Fosfolipídeos/química , ATPase Trocadora de Sódio-Potássio/química , Animais , Sítios de Ligação , Bovinos , Elétrons , Humanos , Proteínas de Membrana/química , Modelos Moleculares , Conformação Molecular , Fosfatidiletanolaminas/química , Fosfoproteínas/química , Ligação Proteica , Proteínas Recombinantes/química , Glycine max/metabolismo , Suínos , Temperatura , Fatores de Tempo
10.
FEBS Lett ; 597(15): 1957-1976, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37357620

RESUMO

Na+ ,K+ -ATPase (NKA) plays a pivotal role in establishing electrochemical gradients for Na+ and K+ across the cell membrane by alternating between the E1 (showing high affinity for Na+ and low affinity for K+ ) and E2 (low affinity to Na+ and high affinity to K+ ) forms. Presented here are two crystal structures of NKA in E1·Mg2+ and E1·3Na+ states at 2.9 and 2.8 Å resolution, respectively. These two E1 structures fill a gap in our description of the NKA reaction cycle based on the atomic structures. We describe how NKA converts the K+ -bound E2·2K+ form to an E1 (E1·Mg2+ ) form, which allows high-affinity Na+ binding, eventually closing the cytoplasmic gate (in E1 ~ P·ADP·3Na+ ) after binding three Na+ , while keeping the extracellular ion pathway sealed. We now understand previously unknown functional roles for several parts of NKA and that NKA uses even the lipid bilayer for gating the ion pathway.


Assuntos
Potássio , ATPase Trocadora de Sódio-Potássio , ATPase Trocadora de Sódio-Potássio/química , Citoplasma/metabolismo , Íons/metabolismo , Citosol/metabolismo , Membrana Celular/metabolismo , Potássio/metabolismo
11.
J Struct Biol ; 177(2): 402-9, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22173220

RESUMO

The structure of full-length human TLR5 determined by electron microscopy single-particle image reconstruction at 26Å resolution shows that TLR5 forms an asymmetric homodimer via ectodomain interactions. The structure shows that like TLR9, TLR5 dimerizes in the absence of ligand. The asymmetry of the dimer suggests that TLR5 may recognize two flagellin molecules cooperatively to establish an optimal flagellin response threshold. A TLR5 homology model was generated and fitted into the electron microscopy structure. All seven predicted N-linked glycosylation sites are exposed on the molecular surface, away from the dimer interface. Glycosylation at the first five sites was confirmed by tandem mass spectrometry. Two aspartate residues proposed to interact with flagellin (Asp294 and Asp366) are sterically occluded by a glycan at position 342. In contrast, the central region of the ectodomains near the dimer interface is unobstructed by glycans. Ligand binding in this region would be consistent with the ligand binding sites of other TLRs.


Assuntos
Flagelina/química , Receptor 5 Toll-Like/química , Glicosilação , Humanos , Modelos Moleculares , Tamanho da Partícula , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica , Processamento de Proteína Pós-Traducional , Estrutura Quaternária de Proteína , Homologia Estrutural de Proteína , Propriedades de Superfície
12.
Open Biol ; 12(4): 210275, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35472286

RESUMO

Cohesin holds sister chromatids together and is cleaved by separase/Cut1 to release DNA during the transition from mitotic metaphase to anaphase. The cohesin complex consists of heterodimeric structural maintenance of chromosomes (SMC) subunits (Psm1 and Psm3), which possess a head and a hinge, separated by long coiled coils. Non-SMC subunits (Rad21, Psc3 and Mis4) bind to the SMC heads. Kleisin/Rad21's N-terminal domain (Rad21-NTD) interacts with Psm3's head-coiled coil junction (Psm3-HCJ). Spontaneous mutations that rescued the cleavage defects in temperature-sensitive (ts) separase mutants were identified in the interaction interface, but the underlying mechanism is yet to be understood. Here, we performed site-directed random mutagenesis to introduce single amino acid substitutions in Psm3-HCJ and Rad21-NTD, and then identified 300 mutations that rescued the cohesin-releasing defects in a separase ts mutant. Mutational analysis indicated that the amino acids involved in hydrophobic cores (which may be in close contact) in Psm3-HCJ and Rad21-NTD are hotspots, since 80 mutations (approx. 27%) were mapped in these locations. Properties of these substitutions indicate that they destabilize the interaction between the Psm3 head and Rad21-NTD. Thus, they may facilitate sister chromatid separation in a cleavage-independent way through cohesin structural re-arrangement.


Assuntos
Anáfase , Proteínas de Schizosaccharomyces pombe , Substituição de Aminoácidos , Proteínas de Ciclo Celular , Proteínas Cromossômicas não Histona , DNA , Proteínas de Schizosaccharomyces pombe/genética , Separase/genética , Coesinas
13.
FEBS Lett ; 596(19): 2513-2524, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35747985

RESUMO

Na+ ,K+ -ATPase (NKA) is one of the most important members of the P-type ion-translocating ATPases and plays a pivotal role in establishing electrochemical gradients for Na+ and K+ across the cell membrane. Presented here is a 3.3 Å resolution structure of NKA in the E2·2K+ state solved by cryo-electron microscopy. It is a stable state with two occluded K+ after transferring three Na+ into the extracellular medium and releasing inorganic phosphate bound to the cytoplasmic P domain. We describe how the extracellular ion pathway wide open in the E2P state becomes closed and locked in E2·2K+ , linked to events at the phosphorylation site more than 50 Å away. We also show, although at low resolution, how ATP binding to NKA in E2·2K+ relaxes the gating machinery and thereby accelerates the transition into the next step, that is, the release of K+ into the cytoplasm, more than 100 times.


Assuntos
ATPase Trocadora de Sódio-Potássio , Sódio , Trifosfato de Adenosina , Microscopia Crioeletrônica , Íons/metabolismo , Fosfatos/metabolismo , Potássio/metabolismo , Sódio/metabolismo , ATPase Trocadora de Sódio-Potássio/química
14.
Nat Struct Mol Biol ; 28(10): 825-834, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34625749

RESUMO

Xkr8-Basigin is a plasma membrane phospholipid scramblase activated by kinases or caspases. We combined cryo-EM and X-ray crystallography to investigate its structure at an overall resolution of 3.8 Å. Its membrane-spanning region carrying 22 charged amino acids adopts a cuboid-like structure stabilized by salt bridges between hydrophilic residues in transmembrane helices. Phosphatidylcholine binding was observed in a hydrophobic cleft on the surface exposed to the outer leaflet of the plasma membrane. Six charged residues placed from top to bottom inside the molecule were essential for scrambling phospholipids in inward and outward directions, apparently providing a pathway for their translocation. A tryptophan residue was present between the head group of phosphatidylcholine and the extracellular end of the path. Its mutation to alanine made the Xkr8-Basigin complex constitutively active, indicating that it plays a vital role in regulating its scramblase activity. The structure of Xkr8-Basigin provides insights into the molecular mechanisms underlying phospholipid scrambling.


Assuntos
Proteínas Reguladoras de Apoptose/química , Basigina/química , Membrana Celular/metabolismo , Proteínas de Membrana/química , Fosfolipídeos/metabolismo , Proteínas Reguladoras de Apoptose/metabolismo , Basigina/metabolismo , Microscopia Crioeletrônica , Humanos , Interações Hidrofóbicas e Hidrofílicas , Proteínas de Membrana/metabolismo , Modelos Moleculares , Complexos Multiproteicos/química , Complexos Multiproteicos/isolamento & purificação , Complexos Multiproteicos/metabolismo , Fosfatidilcolinas/química , Fosfatidilcolinas/metabolismo , Proteínas de Transferência de Fosfolipídeos/química , Proteínas de Transferência de Fosfolipídeos/metabolismo , Fosfolipídeos/química , Estrutura Terciária de Proteína , Triptofano/química
15.
Protein Sci ; 15(3): 468-77, 2006 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-16452622

RESUMO

Maltohexaose-producing amylase (G6-amylase) from alkalophilic Bacillus sp.707 predominantly produces maltohexaose (G6) in the yield of >30% of the total products from short-chain amylose (DP=17). Our previous crystallographic study showed that G6-amylase has nine subsites, from -6 to +3, and pointed out the importance of the indole moiety of Trp140 in G6 production. G6-amylase has very low levels of hydrolytic activities for oligosaccharides shorter than maltoheptaose. To elucidate the mechanism underlying G6 production, we determined the crystal structures of the G6-amylase complexes with G6 and maltopentaose (G5). In the active site of the G6-amylase/G5 complex, G5 is bound to subsites -6 to -2, while G1 and G6 are found at subsites +2 and -7 to -2, respectively, in the G6-amylase/G6 complex. In both structures, the glucosyl residue located at subsite -6 is stacked to the indole moiety of Trp140 within a distance of 4A. The measurement of the activities of the mutant enzymes when Trp140 was replaced by leucine (W140L) or by tyrosine (W140Y) showed that the G6 production from short-chain amylose by W140L is lower than that by W140Y or wild-type enzyme. The face-to-face short contact between Trp140 and substrate sugars is suggested to regulate the disposition of the glucosyl residue at subsite -6 and to govern product specificity for G6 production.


Assuntos
Bacillus/enzimologia , Proteínas de Bactérias/química , Oligossacarídeos/química , Triptofano/química , alfa-Glucosidases/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Domínio Catalítico , Hordeum/enzimologia , Ligantes , Modelos Moleculares , Mutagênese Sítio-Dirigida , Oligossacarídeos/biossíntese , Oligossacarídeos/metabolismo , alfa-Glucosidases/genética , alfa-Glucosidases/metabolismo
16.
Protein Sci ; 13(2): 457-65, 2004 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-14739329

RESUMO

Cyclodextrin glycosyltransferase (CGTase) belonging to the alpha-amylase family mainly catalyzes transglycosylation and produces cyclodextrins from starch and related alpha-1,4-glucans. The catalytic site of CGTase specifically conserves four aromatic residues, Phe183, Tyr195, Phe259, and Phe283, which are not found in alpha-amylase. To elucidate the structural role of Phe283, we determined the crystal structures of native and acarbose-complexed mutant CGTases in which Phe283 was replaced with leucine (F283L) or tyrosine (F283Y). The temperature factors of the region 259-269 in native F283L increased >10 A(2) compared with the wild type. The complex formation with acarbose not only increased the temperature factors (>10 A(2)) but also changed the structure of the region 257-267. This region is stabilized by interactions of Phe283 with Phe259 and Leu260 and plays an important role in the cyclodextrin binding. The conformation of the side-chains of Glu257, Phe259, His327, and Asp328 in the catalytic site was altered by the mutation of Phe283 with leucine, and this indicates that Phe283 partly arranges the structure of the catalytic site through contacts with Glu257 and Phe259. The replacement of Phe283 with tyrosine decreased the enzymatic activity in the basic pH range. The hydroxyl group of Tyr283 forms hydrogen bonds with the carboxyl group of Glu257, and the pK(a) of Glu257 in F283Y may be lower than that in the wild type.


Assuntos
Bacillus/enzimologia , Glucosiltransferases/química , Glucosiltransferases/metabolismo , Fenilalanina/metabolismo , Acarbose/química , Acarbose/metabolismo , Bacillus/classificação , Bacillus/genética , Sítios de Ligação , Domínio Catalítico , Cristalografia por Raios X , Glucosiltransferases/genética , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Cinética , Lisina , Modelos Moleculares , Mutação/genética , Fenilalanina/química , Fenilalanina/genética , Maleabilidade , Estrutura Terciária de Proteína , Especificidade por Substrato , Tirosina
17.
Proteins ; 48(1): 53-62, 2002 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-12012337

RESUMO

The crystal structure of turkey egg lysozyme (TEL) complexed with di-N-acetylchitobiose (NAG2) was refined at 1.19 A resolution by the full-matrix least-squares method with anisotropic temperature factors, and its thermal motion was evaluated by the TLS method. The average ESDs of atomic parameters of nonhydrogen atoms were 0.030 A for coordinates and 0.025 A(2) for anisotropic temperature factors. The active site cleft of TEL binds the alpha-anomer of NAG2 in a nonproductive binding mode with its pyranose rings parallel to a beta-sheet. The TEL structure was compared with the re-refined 1.12 A structure of native TEL. The RMS difference for equivalent Calpha atoms was 0.103 A and a relatively large difference was observed in the region of residues 104-125 rather than in the beta-sheet region where NAG2 was bound. In contrast, the temperature factor of the beta-sheet region was significantly decreased by the NAG2 binding. The TLS model that describes the rigid body motion in translation, libration, and screw motion was adopted for the evaluation of the molecular motion of TEL and NAG2, and the TLS parameters were determined by the least-squares fit to U(ij). The contribution of the external motion of TEL was estimated to be 55.8% of the observed temperature factor for the native structure and 45.9% for the NAG2 complex. The internal motion of TEL represented with atomic thermal ellipsoids was very similar between the native and complex structures except the NAG2 binding region. In the structure of NAG2, the rigid body motion dominates the thermal motion. The center of rotation of NAG2, 4.45A far from the center of gravity, is on the nitrogen atom of the acetylamino group that is hydrogen bonded to the main-chain peptide groups of Asn49 and Ala107. The rigid body motion of NAG2 indicates that the acetylamino group is most strongly bound to the active site, and the recognition of this group is a crucial step of the substrate binding.


Assuntos
Dissacarídeos/química , Dissacarídeos/metabolismo , Modelos Moleculares , Muramidase/química , Muramidase/metabolismo , Animais , Sítios de Ligação , Cristalografia por Raios X , Substâncias Macromoleculares , Movimento (Física) , Ligação Proteica , Termodinâmica , Perus
18.
J Biochem ; 134(6): 881-91, 2003 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-14769878

RESUMO

The stacking interaction between a tyrosine residue and the sugar ring at the catalytic subsite -1 is strictly conserved in the glycoside hydrolase family 13 enzymes. Replacing Tyr100 with leucine in cyclodextrin glycosyltransferase (CGTase) from Bacillus sp. 1011 to prevent stacking significantly decreased all CGTase activities. The adjacent stacking interaction with both Phe183 and Phe259 onto the sugar ring at subsite +2 is essentially conserved among CGTases. F183L/F259L mutant CGTase affects donor substrate binding and/or acceptor binding during transglycosylation [Nakamura et al. (1994) Biochemistry 33, 9929-9936]. To elucidate the precise role of carbohydrate/aromatic stacking interaction at subsites -1 and +2 on the substrate binding of CGTases, we analyzed the X-ray structures of wild-type (2.0 A resolution), and Y100L (2.2 A resolution) and F183L/F259L mutant (1.9 A resolution) CGTases complexed with the inhibitor, acarbose. The refined structures revealed that acarbose molecules bound to the Y100L mutant moved from the active center toward the side chain of Tyr195, and the hydrogen bonding and hydrophobic interaction between acarbose and subsites significantly diminished. The position of pseudo-tetrasaccharide binding in the F183L/F259L mutant was closer to the non-reducing end, and the torsion angles of glycosidic linkages at subsites -1 to +1 on molecule 1 and subsites -2 to -1 on molecule 2 significantly changed compared with that of each molecule of wild-type-acarbose complex to adopt the structural change of subsite +2. These structural and biochemical data suggest that substrate binding in the active site of CGTase is critically affected by the carbohydrate/aromatic stacking interaction with Tyr100 at the catalytic subsite -1 and that this effect is likely a result of cooperation between Tyr100 and Phe259 through stacking interaction with substrate at subsite +2.


Assuntos
Bacillus/enzimologia , Glucosiltransferases/química , Glucosiltransferases/metabolismo , Oligossacarídeos/química , Fenilalanina/química , Tirosina/química , Acarbose/química , Sequência de Aminoácidos , Sítios de Ligação/genética , Cristalografia por Raios X , Glucosiltransferases/genética , Dados de Sequência Molecular , Mutagênese Sítio-Dirigida , Fenilalanina/genética , Ligação Proteica/genética , Relação Estrutura-Atividade , Especificidade por Substrato , Tirosina/genética
19.
Open Biol ; 4(12)2014 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-25520186

RESUMO

Condensin, which contains two structural maintenance of chromosome (SMC) subunits and three regulatory non-SMC subunits, is essential for many chromosomal functions, including mitotic chromosome condensation and segregation. The ATPase domain of the SMC subunit comprises two termini connected by a long helical domain that is interrupted by a central hinge. The role of the ATPase domain has remained elusive. Here we report that the condensin SMC subunit of the fission yeast Schizosaccharomyces pombe is phosphorylated in a manner that requires the presence of the intact SMC ATPase Walker motif. Principal phosphorylation sites reside in the conserved, glycine-rich stretch at the hinge interface surrounded by the highly basic DNA-binding patch. Phosphorylation reduces affinity for DNA. Consistently, phosphomimetic mutants produce severe mitotic phenotypes. Structural evidence suggests that prior opening (though slight) of the hinge is necessary for phosphorylation, which is implicated in condensin's dissociation from and its progression along DNA.


Assuntos
Adenosina Trifosfatases/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , DNA Fúngico/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/genética , Sequência de Aminoácidos , Domínio Catalítico , Proteínas Cromossômicas não Histona/química , Proteínas Cromossômicas não Histona/genética , Sequência Conservada , Proteínas de Ligação a DNA , Modelos Moleculares , Complexos Multiproteicos , Mutação , Fosforilação , Estrutura Secundária de Proteína , Schizosaccharomyces/química , Schizosaccharomyces/enzimologia , Proteínas de Schizosaccharomyces pombe/química , Proteínas de Schizosaccharomyces pombe/genética , Vanadatos/farmacologia
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