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(-) Description

Title :  E. COLI HYDROGENASE-1 VARIANT P508A
 
Authors :  S. B. Carr, S. E. V. Phillips, F. A. Armstrong, R. M. Evans, E. J. Brooke, S. T. A. Islam
Date :  06 May 16  (Deposition) - 08 Mar 17  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  L,M,S,T
Keywords :  Hydrogen Activation, Nife Hydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Brooke, R. M. Evans, S. T. Islam, G. M. Roberts, S. A. Wehlin, S. B. Carr, S. E. Phillips, F. A. Armstrong
Importance Of The Active Site "Canopy" Residues In An O2-Tolerant [Nife]-Hydrogenase.
Biochemistry V. 56 132 2017
PubMed-ID: 28001048  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00868

(-) Compounds

Molecule 1 - HYDROGENASE-1 SMALL CHAIN
    Chains: S, T
    EC Number: 1.12.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K12
    Expression System Taxid: 562
    Gene: HYAA, C1113
    Organism Taxid: 199310
    Synonym: HYD1,MEMBRANE-BOUND HYDROGENASE 1 SMALL SUBUNIT,NIFE HYDROGENASE
 
Molecule 2 - HYDROGENASE-1 LARGE CHAIN
    Chains: L, M
    EC Number: 1.12.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: K12
    Expression System Taxid: 83333
    Gene: HYAB, B0973, JW0955
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: HYD1,MEMBRANE-BOUND HYDROGENASE 1 LARGE SUBUNIT,NIFE HYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : LMST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 21)

Asymmetric/Biological Unit (9, 21)
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
9SO43Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , CYS S:221binding site for residue SF4 S 401
02AC2SOFTWARELYS L:226 , THR S:226 , ASN S:228 , CYS S:230 , TRP S:235 , CYS S:249 , LEU S:250 , CYS S:252binding site for residue F3S S 402
03AC3SOFTWAREHOH L:717 , GLU S:16 , CYS S:17 , CYS S:19 , CYS S:20 , GLU S:76 , THR S:114 , CYS S:115 , CYS S:120 , CYS S:149 , HOH S:671binding site for residue SF3 S 403
04AC4SOFTWARECYS S:120 , GLY S:256 , HOH S:595binding site for residue CL S 404
05AC5SOFTWAREILE S:12 , HIS S:13 , ASP S:46 , LYS S:98 , HOH S:549binding site for residue CL S 405
06AC6SOFTWARECSO L:79 , VAL L:82 , HIS L:83 , ALA L:507 , ALA L:508 , ARG L:509 , VAL L:530 , PRO L:531 , THR L:532 , CYS L:576 , CYS L:579 , NI L:602 , HOH L:949binding site for residue FCO L 601
07AC7SOFTWARECYS L:76 , CSO L:79 , CYS L:576 , CYS L:579 , FCO L:601 , HOH L:949binding site for residue NI L 602
08AC8SOFTWAREGLU L:57 , CYS L:528 , HIS L:582 , HOH L:726 , HOH L:727 , HOH L:730binding site for residue MG L 603
09AC9SOFTWARELEU L:482 , ALA L:483 , ARG S:211binding site for residue SO4 L 604
10AD1SOFTWARELYS L:157 , HOH L:750 , HOH L:992 , LYS M:157binding site for residue SO4 L 605
11AD2SOFTWAREHIS T:187 , CYS T:190 , ARG T:193 , CYS T:215 , LEU T:216 , CYS T:221binding site for residue SF4 T 401
12AD3SOFTWARELYS 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
13AD4SOFTWAREHOH M:720 , GLU T:16 , CYS T:17 , CYS T:19 , CYS T:20 , GLU T:76 , THR T:114 , CYS T:115 , CYS T:120 , CYS T:149 , HOH T:611binding site for residue SF3 T 403
14AD5SOFTWARECYS T:120 , GLY T:256 , HOH T:622binding site for residue CL T 404
15AD6SOFTWAREILE T:12 , HIS T:13 , ASP T:46 , LYS T:98 , HOH T:570 , HOH T:673binding site for residue CL T 405
16AD7SOFTWARECSO M:79 , VAL M:82 , HIS M:83 , ALA M:507 , ALA M:508 , ARG M:509 , VAL M:530 , PRO M:531 , THR M:532 , CYS M:576 , CYS M:579 , NI M:602 , HOH M:918binding site for residue FCO M 601
17AD8SOFTWARECYS M:76 , CSO M:79 , CYS M:576 , CYS M:579 , FCO M:601 , HOH M:918binding site for residue NI M 602
18AD9SOFTWAREGLU M:57 , CYS M:528 , HIS M:582 , HOH M:715 , HOH M:718 , HOH M:733binding site for residue MG M 603
19AE1SOFTWAREARG M:394 , ARG S:125binding site for residue SO4 M 604

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1L:76 -L:79
2M:76 -M:79

(-) Cis Peptide Bonds  (10, 11)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JRD)

(-) 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...............................eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhh.........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jrd L   2 STQYETQGYTINNAGRRLVVDPITRIEGHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGRDPRDAWAFVERICGVcTGVHALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHDHLVHFYQLAGMDWIDVLDALKADPRKTSELAQSLSSWPKSSPGYFFDVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQREIVKIHAVFGGKNPHPNWIVGGMPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGLSDKCVLSYGAFPDIANDFGEKSLLMPGGAVINGDFNNVLPVDLVDPQQVQEFVDHAWYRYPNDQVGRHPFDGITDPWYNPGDVKGSDTNIQQLNEQERYSWIKAPRWRGNAMEVGPLARTLIAYHKGDAATVESVDRMMSALNLPLSGIQSTLGRILCRAHEAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAARGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKMAIPEQPLEILRTLHSFDPCLACSTH 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.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhh.........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jrd M   2 STQYETQGYTINNAGRRLVVDPITRIEGHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGRDPRDAWAFVERICGVcTGVHALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHDHLVHFYQLAGMDWIDVLDALKADPRKTSELAQSLSSWPKSSPGYFFDVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQREIVKIHAVFGGKNPHPNWIVGGMPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGLSDKCVLSYGAFPDIANDFGEKSLLMPGGAVINGDFNNVLPVDLVDPQQVQEFVDHAWYRYPNDQVGRHPFDGITDPWYNPGDVKGSDTNIQQLNEQERYSWIKAPRWRGNAMEVGPLARTLIAYHKGDAATVESVDRMMSALNLPLSGIQSTLGRILCRAHEAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAARGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKMAIPEQPLEILRTLHSFDPCLACSTH 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
                 5jrd 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.hhhhh..hhhhhhhh.......hhhhhh...hhhhh.hhhhh.............................hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jrd 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)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5JRD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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  5jrd
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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 5a4f 5a4i 5a4m 5adu
        MBHS_ECOLI | P69739: 3uqy 3usc 3use 4gd3 4ue3 5a4f 5a4i 5a4m 5adu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JRD)