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(-) Description

Title :  THE MECHANISM OF HYDROGEN ACTIVATION BY NIFE-HYDROGENASES AND THE IMPORTANCE OF THE ACTIVE SITE ARGININE
 
Authors :  R. M. Evans, S. A. M. Wehlin, E. Nomerotskaia, F. Sargent, S. B. Carr, S. E. V. Phillips, F. A. Armstrong
Date :  15 Dec 14  (Deposition) - 24 Dec 14  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  L,M,S,T
Keywords :  Membrane-Bound Hydrogenase, Oxidoreductase, Ni-Fe Hydrogenase, Hydrogen (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: S, T
    EC Number: 1.12.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: FTH004
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MC4100
    Synonym: HYD1, MEMBRANE-BOUND HYDROGENASE 1 LARGE SUBUNIT, NIFE HYDROGENASE
 
Molecule 2 - HYDROGENASE-1 SMALL CHAIN
    Chains: L, M
    EC Number: 1.12.99.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: MUTATION R509K IN LARGE SUBUNIT
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN, RESIDUES 46-372
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MC4100
    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  (7, 18)

Asymmetric/Biological Unit (7, 18)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2F3S2Ligand/IonFE3-S4 CLUSTER
3MG2Ligand/IonMAGNESIUM ION
4NFV2Ligand/IonNI-FE OXIDIZED ACTIVE CENTER
5SF32Ligand/IonFE4-S3 CLUSTER
6SF42Ligand/IonIRON/SULFUR CLUSTER
7SO44Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS L:76 , CYS L:79 , VAL L:82 , HIS L:83 , ALA L:507 , PRO L:508 , LYS L:509 , LEU L:512 , VAL L:530 , PRO L:531 , THR L:532 , CYS L:576 , CYS L:579BINDING SITE FOR RESIDUE NFV L 601
02AC2SOFTWAREGLU L:57 , CYS L:528 , HIS L:582 , HOH L:2045 , HOH L:2046 , HOH L:2289BINDING SITE FOR RESIDUE MG L 603
03AC3SOFTWARECYS M:76 , CYS M:79 , VAL M:82 , HIS M:83 , ALA M:507 , PRO M:508 , LYS M:509 , LEU M:512 , VAL M:530 , PRO M:531 , THR M:532 , CYS M:576 , CYS M:579BINDING SITE FOR RESIDUE NFV M 601
04AC4SOFTWAREGLU M:57 , CYS M:528 , HIS M:582 , HOH M:2058 , HOH M:2059 , HOH M:2310BINDING SITE FOR RESIDUE MG M 603
05AC5SOFTWAREARG M:394 , ARG S:125BINDING SITE FOR RESIDUE SO4 M 604
06AC6SOFTWAREHIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , CYS S:221BINDING SITE FOR RESIDUE SF4 S 401
07AC7SOFTWARELYS 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
08AC8SOFTWAREGLU S:16 , CYS S:17 , CYS S:19 , THR S:114 , CYS S:115 , CYS S:120 , GLY S:148 , CYS S:149BINDING SITE FOR RESIDUE SF3 S 403
09AC9SOFTWARETHR S:114 , TRP S:118 , CYS S:120 , GLY S:256 , HOH S:2055BINDING SITE FOR RESIDUE CL S 405
10BC1SOFTWAREILE S:12 , HIS S:13 , ASP S:46 , LYS S:98 , HOH S:2002BINDING SITE FOR RESIDUE CL S 406
11BC2SOFTWAREASN L:481 , LEU L:482 , ALA L:483 , ARG S:211BINDING SITE FOR RESIDUE SO4 S 407
12BC3SOFTWAREHIS T:187 , CYS T:190 , ARG T:193 , CYS T:215 , LEU T:216 , CYS T:221BINDING SITE FOR RESIDUE SF4 T 401
13BC4SOFTWARELYS 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
14BC5SOFTWAREGLU T:16 , CYS T:17 , CYS T:19 , THR T:114 , CYS T:115 , CYS T:120 , GLY T:148 , CYS T:149BINDING SITE FOR RESIDUE SF3 T 403
15BC6SOFTWARETRP T:118 , CYS T:120 , GLY T:256 , HOH T:2046BINDING SITE FOR RESIDUE CL T 405
16BC7SOFTWAREILE T:12 , HIS T:13 , ASP T:46 , LYS T:98 , HOH T:2003BINDING SITE FOR RESIDUE CL T 406
17BC8SOFTWAREHOH L:2151 , GLY M:480 , ASN M:481 , LEU M:482 , ALA M:483 , ARG T:211BINDING SITE FOR RESIDUE SO4 T 408
18BC9SOFTWARELYS T:218 , ARG T:266BINDING SITE FOR RESIDUE SO4 T 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UE3)

(-) 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 4UE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UE3)

(-) Exons   (0, 0)

(no "Exon" information available for 4UE3)

(-) 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.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhh.........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ue3 L   2 STQYETQGYTINNAGRRLVVDPITRIEGHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGRDPRDAWAFVERICGVCTGVHALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHDHLVHFYQLAGMDWIDVLDALKADPRKTSELAQSLSSWPKSSPGYFFDVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQREIVKIHAVFGGKNPHPNWIVGGMPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGLSDKCVLSYGAFPDIANDFGEKSLLMPGGAVINGDFNNVLPVDLVDPQQVQEFVDHAWYRYPNDQVGRHPFDGITDPWYNPGDVKGSDTNIQQLNEQERYSWIKAPRWRGNAMEVGPLARTLIAYHKGDAATVESVDRMMSALNLPLSGIQSTLGRILCRAHEAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAPKGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKMAIPEQPLEILRTLHSFDPCLACSTH 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 


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
                 4ue3 M   2 STQYETQGYTINNAGRRLVVDPITRIEGHMRCEVNINDQNVITNAVSCGTMFRGLEIILQGRDPRDAWAFVERICGVCTGVHALASVYAIEDAIGIKVPDNANIIRNIMLATLWCHDHLVHFYQLAGMDWIDVLDALKADPRKTSELAQSLSSWPKSSPGYFFDVQNRLKKFVEGGQLGIFRNGYWGHPQYKLPPEANLMGFAHYLEALDFQREIVKIHAVFGGKNPHPNWIVGGMPCAINIDESGAVGAVNMERLNLVQSIITRTADFINNVMIPDALAIGQFNKPWSEIGTGLSDKCVLSYGAFPDIANDFGEKSLLMPGGAVINGDFNNVLPVDLVDPQQVQEFVDHAWYRYPNDQVGRHPFDGITDPWYNPGDVKGSDTNIQQLNEQERYSWIKAPRWRGNAMEVGPLARTLIAYHKGDAATVESVDRMMSALNLPLSGIQSTLGRILCRAHEAQWAAGKLQYFFDKLMTNLKNGNLATASTEKWEPATWPTECRGVGFTEAPKGALGHWAAIRDGKIDLYQCVVPTTWNASPRDPKGQIGAYEAALMNTKMAIPEQPLEILRTLHSFDPCLACSTH 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 


Chain S from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               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
                 4ue3 S   4 KPRIPVVWIHGLECTCCTESFIRSAHPLAKDVILSLISLDYDDTLMAAAGTQAEEVFEDIITQYNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAAAGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYMVTFDRLPDVDRMGRPLMFYGQRIHDKCYRRAHFDAGEFVQSWDDDAARKGYCLYKMGCKGPTTYNACSSTRWNDGVSFPIQSGHGCLGCAENGFWDRGSFYSRVV 268
                                    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:265
                                                                                                                                                                                                                                                                                                         
               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..hhhhhhhh.......hhhhhh...hhhhh.hhhhh.............................hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ue3 T   4 KPRIPVVWIHGLECTCCTESFIRSAHPLAKDVILSLISLDYDDTLMAAAGTQAEEVFEDIITQYNGKYILAVEGNPPLGEQGMFCISSGRPFIEKLKRAAAGASAIIAWGTCASWGCVQAARPNPTQATPIDKVITDKPIIKVPGCPPIPDVMSAIITYMVTFDRLPDVDRMGRPLMFYGQRIHDKCYRRAHFDAGEFVQSWDDDAARKGYCLYKMGCKGPTTYNACSSTRWNDGVSFPIQSGHGCLGCAENGFWDRGSFYSRVV 268
                                    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 4UE3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UE3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UE3)

(-) Gene Ontology  (20, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

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