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(-) Description

Title :  STRUCTURE OF THE OXIDISED, AS-ISOLATED NIFESE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH
 
Authors :  M. C. Marques, R. Coelho, A. L. Delacey, I. A. C. Pereira, P. M. Matias
Date :  07 Aug 09  (Deposition) - 12 Jan 10  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrogenase, Metal-Binding, Oxidoreductase, Oxygen Tolerance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Marques, R. Coelho, A. L. De Lacey, I. A. C. Pereira, P. M. Matias
The Three-Dimensional Structure Of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough: A Hydrogenase Without A Bridging Ligand In The Active Site In Its Oxidised, "As- Isolated" State.
J. Mol. Biol. V. 396 893 2010
PubMed-ID: 20026074  |  Reference-DOI: 10.1016/J.JMB.2009.12.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
    Atcc: 29579
    Chains: A
    EC Number: 1.18.99.1
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH
    Synonym: NIFESE HYDROGENASE
 
Molecule 2 - PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
    Atcc: 29579
    Chains: B
    EC Number: 1.18.99.1
    Fragment: RESIDUES 1-495
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH
    Synonym: NIFESE HYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 14)

Asymmetric/Biological Unit (9, 14)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FCO1Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
3FE21Ligand/IonFE (II) ION
4FSX1Ligand/IonBIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
5NI1Ligand/IonNICKEL (II) ION
6OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
7PSW1Mod. Amino Acid3-(SULFANYLSELANYL)-L-ALANINE
8SBY4Ligand/Ion3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
9SF43Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:208 , CYS A:211 , TYR A:213 , LEU A:214 , TYR A:217 , CYS A:232 , ARG A:233 , TYR A:234 , CYS A:238 , GLY A:240 , VAL A:260BINDING SITE FOR RESIDUE SF4 A1284
02AC2SOFTWARETHR A:243 , CYS A:247 , TRP A:252 , CYS A:259 , CYS A:265 , ILE A:266 , CYS A:268 , ARG B:182 , GLN B:187BINDING SITE FOR RESIDUE SF4 A1285
03AC3SOFTWARECYS A:18 , THR A:19 , GLY A:20 , CYS A:21 , GLU A:77 , GLY A:119 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , HOH A:2031 , HIS B:185BINDING SITE FOR RESIDUE FSX A1287
04AC4SOFTWAREGLY A:17 , CYS A:18 , CYS A:21 , GLY A:119 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , ARG B:73 , HIS B:185BINDING SITE FOR RESIDUE SF4 A1286
05AC5SOFTWARESER A:22 , LEU A:37 , GLU B:167BINDING SITE FOR RESIDUE SBY A1288
06AC6SOFTWAREPHE A:73 , VAL A:170BINDING SITE FOR RESIDUE SBY A1289
07AC7SOFTWARECYS B:78 , HIS B:82 , ALA B:420 , PRO B:421 , ARG B:422 , LEU B:425 , ALA B:444 , SER B:445 , PSW B:489 , CYS B:492 , NI B:1498BINDING SITE FOR RESIDUE FCO B1497
08AC8SOFTWAREOCS B:75 , CYS B:78 , SEC B:489 , PSW B:489 , CYS B:492 , FCO B:1497BINDING SITE FOR RESIDUE NI B1498
09AC9SOFTWAREGLU B:56 , ILE B:441 , HIS B:495 , HOH B:2031 , HOH B:2119 , HOH B:2120BINDING SITE FOR RESIDUE FE2 B1499
10BC1SOFTWARECYS B:78 , THR B:80 , ALA B:81 , PHE B:110 , ASN B:113 , PRO B:421BINDING SITE FOR RESIDUE CL B1500
11BC2SOFTWAREGLN B:128 , VAL B:131 , PRO B:134 , PHE B:139 , TYR B:162BINDING SITE FOR RESIDUE SBY B1501
12BC3SOFTWARETYR B:162BINDING SITE FOR RESIDUE SBY B1502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WPN)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Cys A:159 -Pro A:160
2Phe A:273 -Pro A:274
3Ser A:278 -Pro A:279
4Asp B:22 -Pro B:23
5Ala B:137 -Pro B:138
6Val B:140 -Pro B:141
7Met B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WPN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WPN)

(-) Exons   (0, 0)

(no "Exon" information available for 2WPN)

(-) 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 A from PDB  Type:PROTEIN  Length:277
 aligned with Q72AS4_DESVH | Q72AS4 from UniProtKB/TrEMBL  Length:317

    Alignment length:277
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
         Q72AS4_DESVH    41 RPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA 317
               SCOP domains d2wpna_ A: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2wpnA01 A:7-202  [code=3.40.50.700, no name defined]                                                                                                                                                2wpnA02 A:203-283 Cytochrome-c3 Hydrogenase, chain A, domain 2                    CATH domains
               Pfam domains -----------Oxidored_q6-2wpnA01 A:18-173                                                                                                                                -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......hhhhhhh....hhhhhhhhh.eeee.........hhhhhhhhhhhhhh...eeeee.......................hhhhhhhhh...eeeeee.....................hhhhhh........eee......hhhhhh.hhhhhhhhhhhh.....hhhhhh...............hhhhh.hhhhhhh..........................hhhhhh......hhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wpn A   7 RPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA 283
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       


Chain B from PDB  Type:PROTEIN  Length:481
 aligned with Q72AS3_DESVH | Q72AS3 from UniProtKB/TrEMBL  Length:510

    Alignment length:481
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 
         Q72AS3_DESVH    15 GRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPULGCAVH 495
               SCOP domains d2wpnb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2wpnB00 B:15-495 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------NiFeSe_Hases-2wpnB01 B:141-495                                                                                                                                                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------NiFeSe_Hases-2wpnB02 B:141-495                                                                                                                                                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ..eeeee..........eeeeee....eeeeeee..............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh....................hhhhhhh.hhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh......................................hhh.eeee......hhhhh.......................eeee........hhhhhhhhh.......hhhhhhhh......hhhh..........hhhhhhhhhhhhh.......................................eeeeeee..eeeeeeeehhhhhhh..........hhhhhh...........hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wpn B  15 GRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRIcGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPxLGCAVH 495
                                    24        34        44        54        64        74|       84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    |  494 
                                                                                       75-OCS                                                                                                                                                                                                                                                                                                                                                                                                                       489-PSW
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: NiFeSe_Hases] (17)
(-)
Clan: no clan defined [family: Oxidored_q6] (18)

(-) Gene Ontology  (9, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q72AS4_DESVH | Q72AS4)
molecular function
    GO:0051538    3 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0009375    ferredoxin hydrogenase complex    An enzyme complex that catalyzes the oxidation of reduced ferredoxin. Hydrogenase contains iron-sulfur clusters, and some contain nickel; it can use molecular hydrogen for the reduction of a variety of substances.

Chain B   (Q72AS3_DESVH | Q72AS3)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016151    nickel cation binding    Interacting selectively and non-covalently with nickel (Ni) cations.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  2wpn
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 Related Entries

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

UniProtKB/TrEMBL
        Q72AS3_DESVH | Q72AS3: 3ze6 3ze7 3ze8 3ze9 3zea 5jsh 5jsk 5jsu 5jsy 5jt1
        Q72AS4_DESVH | Q72AS4: 3ze6 3ze7 3ze8 3ze9 3zea 5jsh 5jsk 5jsu 5jsy 5jt1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WPN)