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(-) Description

Title :  THE MECHANISM OF HYDROGEN ACTIVATION BY NIFE-HYDROGENASES.
 
Authors :  R. M. Evans, E. J. Brooke, S. A. M. Wehlin, E. Nomerotskaia, F. Sargent, S S. E. V. Phillips, F. A. Armstrong
Date :  09 Jun 15  (Deposition) - 25 Nov 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  L,M,S,T
Keywords :  Oxidoreductase, Nife-Hydrogenase, Hydrogen Lysis, Redox, Fes Cluster, Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Evans, E. J. Brooke, S. A. Wehlin, E. Nomerotskaia, F. Sargent, S. B. Carr, S. E. Phillips, F. A. Armstrong
Mechanism Of Hydrogen Activation By [Nife] Hydrogenases.
Nat. Chem. Biol. V. 12 46 2016
PubMed-ID: 26619250  |  Reference-DOI: 10.1038/NCHEMBIO.1976

(-) Compounds

Molecule 1 - HYDROGENASE-1 LARGE CHAIN
    Chains: L, M
    EC Number: 1.12.99.6
    Fragment: CATALYTIC DOMAIN, RESIDUES 1-582
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100
    Organism Taxid: 1403831
    Synonym: HYD1, MEMBRANE-BOUND HYDROGENASE 1 LARGE SUBUNIT, NIFE HYDROGENASE
 
Molecule 2 - HYDROGENASE-1 SMALL CHAIN
    Chains: S, T
    EC Number: 1.12.99.6
    Fragment: RESIDUES 46-372
    Organism Scientific: ESCHERICHIA COLI STR. K-12 SUBSTR. MC4100
    Organism Taxid: 1403831
    Synonym: HYD1, MEMBRANE-BOUND HYDROGENASE 1 SMALL SUBUNIT, NIFE HYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : LMST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 20)

Asymmetric/Biological Unit (9, 20)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3F3S2Ligand/IonFE3-S4 CLUSTER
4FCO2Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
5MG2Ligand/IonMAGNESIUM ION
6NI2Ligand/IonNICKEL (II) ION
7SF32Ligand/IonFE4-S3 CLUSTER
8SF42Ligand/IonIRON/SULFUR CLUSTER
9SO42Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECSO L:79 , VAL L:82 , HIS L:83 , ALA L:507 , PRO L:508 , ARG L:509 , LEU L:512 , VAL L:530 , PRO L:531 , THR L:532 , CYS L:579 , NI L:602 , HOH L:2071BINDING SITE FOR RESIDUE FCO L 601
02AC2SOFTWARECYS L:76 , CSO L:79 , CYS L:576 , CYS L:579 , FCO L:601 , HOH L:2071BINDING SITE FOR RESIDUE NI L 602
03AC3SOFTWAREGLU L:57 , CYS L:528 , HIS L:582 , HOH L:2050 , HOH L:2051 , HOH L:2263BINDING SITE FOR RESIDUE MG L 603
04AC4SOFTWARECSO M:79 , VAL M:82 , HIS M:83 , ALA M:507 , PRO M:508 , ARG M:509 , LEU M:512 , VAL M:530 , PRO M:531 , THR M:532 , CYS M:579 , NI M:602 , HOH M:2074BINDING SITE FOR RESIDUE FCO M 601
05AC5SOFTWARECYS M:76 , CSO M:79 , CYS M:576 , CYS M:579 , FCO M:601 , HOH M:2074BINDING SITE FOR RESIDUE NI M 602
06AC6SOFTWAREGLU M:57 , CYS M:528 , HIS M:582 , HOH M:2050 , HOH M:2051 , HOH M:2269BINDING SITE FOR RESIDUE MG M 603
07AC7SOFTWAREARG M:394 , ARG S:125BINDING SITE FOR RESIDUE SO4 M 604
08AC8SOFTWAREHIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , CYS S:221BINDING SITE FOR RESIDUE SF4 S 401
09AC9SOFTWARELYS L:226 , THR S:226 , ASN S:228 , CYS S:230 , TRP S:235 , PRO S:242 , CYS S:249 , LEU S:250 , CYS S:252BINDING SITE FOR RESIDUE F3S S 402
10BC1SOFTWAREGLU S:16 , CYS S:17 , THR S:18 , CYS S:19 , THR S:114 , CYS S:115 , CYS S:120 , GLY S:148 , CYS S:149 , HOH S:2003BINDING SITE FOR RESIDUE SF3 S 403
11BC2SOFTWARETRP S:118 , CYS S:120 , GLY S:256 , HOH S:2046 , HOH S:2048BINDING SITE FOR RESIDUE CL S 405
12BC3SOFTWAREHOH L:2030 , ILE S:12 , HIS S:13 , ASP S:46 , LYS S:98 , HOH S:2002BINDING SITE FOR RESIDUE CL S 406
13BC4SOFTWAREGLY L:480 , ASN L:481 , LEU L:482 , ALA L:483 , ARG S:211BINDING SITE FOR RESIDUE SO4 S 407
14BC5SOFTWAREHIS T:187 , CYS T:190 , ARG T:193 , CYS T:215 , LEU T:216 , CYS T:221BINDING SITE FOR RESIDUE SF4 T 401
15BC6SOFTWARELYS M:226 , THR T:226 , ASN T:228 , CYS T:230 , TRP T:235 , PRO T:242 , CYS T:249 , LEU T:250 , CYS T:252BINDING SITE FOR RESIDUE F3S T 402
16BC7SOFTWAREGLU T:16 , CYS T:17 , THR T:18 , CYS T:19 , THR T:114 , CYS T:115 , CYS T:120 , GLY T:148 , CYS T:149 , HOH T:2005BINDING SITE FOR RESIDUE SF3 T 403
17BC8SOFTWARETRP T:118 , CYS T:120 , GLY T:256 , HOH T:2039BINDING SITE FOR RESIDUE CL T 405
18BC9SOFTWAREILE T:12 , HIS T:13 , ASP T:46 , LYS T:98BINDING SITE FOR RESIDUE CL T 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A4F)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Asp L:22 -Pro L:23
2Asn L:227 -Pro L:228
3Asp M:22 -Pro M:23
4Asn M:227 -Pro M:228
5His S:29 -Pro S:30
6Arg S:125 -Pro S:126
7Cys S:149 -Pro S:150
8His T:29 -Pro T:30
9Arg T:125 -Pro T:126
10Cys T:149 -Pro T:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A4F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A4F)

(-) Exons   (0, 0)

(no "Exon" information available for 5A4F)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain L from PDB  Type:PROTEIN  Length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee...eeeee.........eeeeeee.....eeeeeeee....hhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eee..eee..........eee..eee..................eeee...............hhhhh...........eee..eeee...........eeee.......hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhh.........hhhhhhhh.........hhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a4f L   2 STQYETQGYTINNAGRRLVVDPITRIEGHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGRDPRDAWAFVERICGVcTGVHALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHAHLVHFYQLAGMDWIDVLDALKADPRKTSELAQSLSSWPKSSPGYFFDVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQREIVKIHAVFGGKNPHPNWIVGGMPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGLSDKCVLSYGAFPDIANDFGEKSLLMPGGAVINGDFNNVLPVDLVDPQQVQEFVDHAWYRYPNDQVGRHPFDGITDPWYNPGDVKGSDTNIQQLNEQERYSWIKAPRWRGNAMEVGPLARTLIAYHKGDAATVESVDRMMSALNLPLSGIQSTLGRILCRAHEAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAPRGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKMAIPEQPLEILRTLHSFDPCLACSTH 582
                                    11        21        31        41        51        61        71       |81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581 
                                                                                                        79-CSO                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain M from PDB  Type:PROTEIN  Length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee...eeeee.........eeeeeee.....eeeeeeee....hhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eee..eee..........eee..eee..................eeee...............hhhhh...........eee..eeee...........eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhh.........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a4f M   2 STQYETQGYTINNAGRRLVVDPITRIEGHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGRDPRDAWAFVERICGVcTGVHALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHAHLVHFYQLAGMDWIDVLDALKADPRKTSELAQSLSSWPKSSPGYFFDVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQREIVKIHAVFGGKNPHPNWIVGGMPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGLSDKCVLSYGAFPDIANDFGEKSLLMPGGAVINGDFNNVLPVDLVDPQQVQEFVDHAWYRYPNDQVGRHPFDGITDPWYNPGDVKGSDTNIQQLNEQERYSWIKAPRWRGNAMEVGPLARTLIAYHKGDAATVESVDRMMSALNLPLSGIQSTLGRILCRAHEAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAPRGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKMAIPEQPLEILRTLHSFDPCLACSTH 582
                                    11        21        31        41        51        61        71       |81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581 
                                                                                                        79-CSO                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain S from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhh....hhhhhhhhheeeeee......hhhhhhhhhhhhhhhh...eeeeee....hhhhhh..ee..eehhhhhhhhhhheeeeeeehhhhhh.hhhhh........hhhhh.....eeee.....hhhhhhhhhhhhhhhh..........hhhhhh..hhhhh.hhhhhhhh.......hhhhhh...hhhhh.hhhhh.............................hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a4f S   4 KPRIPVVWIHGLECTCCTESFIRSAHPLAKDVILSLISLDYDDTLMAAAGTQAEEVFEDIITQYNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAAAGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYMVTFDRLPDVDRMGRPLMFYGQRIHDKCYRRAHFDAGEFVQSWDDDAARKGYCLYKMGCKGPTTYNACSSTRWNDGVSFPIQSGHGCLGCAENGFWDRGSFYSRV 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    


Chain T from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhh....hhhhhhhhheeeeee......hhhhhhhhhhhhhhhh...eeeeee....hhhhhh..ee..eehhhhhhhhhhheeeeeeehhhhhh.hhhhh........hhhhh.....eeee.....hhhhhhhhhhhhhhhh..........hhhhhh..hhhh..hhhhhhh........hhhhhh...hhhhh.hhhhh.............................hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a4f T   4 KPRIPVVWIHGLECTCCTESFIRSAHPLAKDVILSLISLDYDDTLMAAAGTQAEEVFEDIITQYNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAAAGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYMVTFDRLPDVDRMGRPLMFYGQRIHDKCYRRAHFDAGEFVQSWDDDAARKGYCLYKMGCKGPTTYNACSSTRWNDGVSFPIQSGHGCLGCAENGFWDRGSFYSRV 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5A4F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A4F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A4F)

(-) Gene Ontology  (20, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  MBHS_ECOLI | P69739
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MBHL_ECOLI | P0ACD8: 3uqy 3usc 3use 4gd3 4ue3 5a4i 5a4m 5adu 5jrd
        MBHS_ECOLI | P69739: 3uqy 3usc 3use 4gd3 4ue3 5a4i 5a4m 5adu 5jrd

(-) Related Entries Specified in the PDB File

5a4i MECHANISM OF HYDROGEN ACTIVATION BY NIFE-HYDROGENASES
5a4m MECHANISM OF HYDROGEN ACTIVATION BY NIFE-HYDROGENASES