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(-) Description

Title :  CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM
 
Authors :  E. Garcin, X. Vernede, E. C. Hatchikian, A. Volbeda, M. Frey, J. C. Fonte Camps
Date :  03 Mar 99  (Deposition) - 01 Jun 99  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  L,S
Keywords :  Ni-Fe-Se Hydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Garcin, X. Vernede, E. C. Hatchikian, A. Volbeda, M. Frey, J. C. Fontecilla-Camps
The Crystal Structure Of A Reduced [Nifese] Hydrogenase Provides An Image Of The Activated Catalytic Center
Structure Fold. Des. V. 7 557 1999
PubMed-ID: 10378275  |  Reference-DOI: 10.1016/S0969-2126(99)80072-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROGENASE (SMALL SUBUNIT)
    Cellular Location: PERIPLASM
    Chains: S
    EC Number: 1.18.99.1
    Organism Scientific: DESULFOMICROBIUM BACULATUM
    Organism Taxid: 899
    Strain: WILD TYPE
    Synonym: CYTOCHROME C3 HYDROGENASE
 
Molecule 2 - HYDROGENASE (LARGE SUBUNIT)
    Cellular Location: PERIPLASM
    Chains: L
    EC Number: 1.18.99.1
    Organism Scientific: DESULFOMICROBIUM BACULATUM
    Organism Taxid: 899
    Other Details: COMPLEXED WITH IRON/SULFUR CLUSTER, CARBONMONOXIDE- (DICYANO) IRON, HYDROSULFURIC ACID
    Strain: WILD TYPE
    Synonym: CYTOCHROME C3 HYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : LS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1FCO1Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
2FE21Ligand/IonFE (II) ION
3H2S1Ligand/IonHYDROSULFURIC ACID
4NI1Ligand/IonNICKEL (II) ION
5SEC1Mod. Amino Acid
6SF43Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS L:70 , CYS L:73 , SEC L:492 , CYS L:495 , FCO L:499BINDING SITE FOR RESIDUE NI L 500
2AC2SOFTWAREGLU L:51 , ILE L:444 , HIS L:498 , HOH L:519 , HOH L:523 , HOH L:541BINDING SITE FOR RESIDUE FE2 L 501
3AC3SOFTWAREHIS S:208 , CYS S:211 , TYR S:213 , LEU S:214 , CYS S:231 , LYS S:232 , CYS S:237 , VAL S:259BINDING SITE FOR RESIDUE SF4 S 284
4AC4SOFTWAREARG L:185 , GLN L:190 , THR S:242 , CYS S:246 , TRP S:251 , CYS S:258 , CYS S:264 , ILE S:265 , CYS S:267BINDING SITE FOR RESIDUE SF4 S 285
5AC5SOFTWAREARG L:68 , HIS L:188 , CYS S:18 , CYS S:21 , GLY S:124 , THR S:125 , CYS S:126 , GLY S:163 , CYS S:164 , PRO S:165BINDING SITE FOR RESIDUE SF4 S 286
6AC6SOFTWARECYS L:73 , HIS L:77 , ALA L:423 , PRO L:424 , ARG L:425 , LEU L:428 , ALA L:447 , THR L:448 , SEC L:492 , CYS L:495 , NI L:500BINDING SITE FOR RESIDUE FCO L 499
7AC7SOFTWARECYS L:73 , THR L:75 , ALA L:76 , PHE L:105 , ASN L:108 , PRO L:424BINDING SITE FOR RESIDUE H2S L 502
8ACTAUTHORCYS L:70 , CYS L:73 , SEC L:492 , CYS L:495 , FCO L:499 , NI L:500NI-FE ACTIVE SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CC1)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1His S:30 -Pro S:31
2Cys S:164 -Pro S:165
3Phe S:272 -Pro S:273
4Ser S:277 -Pro S:278
5Asp L:17 -Pro L:18
6Ser L:132 -Pro L:133
7Val L:135 -Pro L:136
8Met L:186 -Pro L:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CC1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NI_HGENASE_L_1PS00507 Nickel-dependent hydrogenases large subunit signature 1.PHSL_DESBA49-74  1L:48-73
2NI_HGENASE_L_2PS00508 Nickel-dependent hydrogenases large subunit signature 2.PHSL_DESBA490-499  1L:489-498

(-) Exons   (0, 0)

(no "Exon" information available for 1CC1)

(-) 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:487
 aligned with PHSL_DESBA | P13065 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:487
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       
           PHSL_DESBA    13 VKISIDPLTRVEGHLKIEVEVKDGKVVDAKCSGGMFRGFEQILRGRDPRDSSQIVQRICGVCPTAHCTASVMAQDDAFGVKVTTNGRITRNLIFGANYLQSHILHFYHLAALDYVKGPDVSPFVPRYANADLLTDRIKDGAKADATNTYGLNQYLKALEIRRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEYAARFKEVQKFVIEEYLPLIYTLGSVYTDLFETGIGWKNVIAFGVFPEDDDYKTFLLKPGVYIDGKDEEFDSKLVKEYVGHSFFDHSAPGGLHYSVGETNPNPDKPGAYSFVKAPRYKDKPCEVGPLARMWVQNPELSPVGQKLLKELYGIEAKKFRDLGDKAFSIMGRHVLVAEETWLTAVAVEKWLKQVQPGAETYVKSEIPDAAEGTGFTEAPRGALLHYLKIKDKKIENYQIVSATLWNANPRDDMGQRGPIEEALIGVPVPDIKNPVNVGRLVRSYDPULGCAVH 499
               SCOP domains d1cc1l_ L: Nickel-iron hydrogenase, large subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1cc1L00 L:12-498 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeeeee..eeeeeeeee....hhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee..eee.......eee..eeee..eee..hhh.eeee.............ee.hhh................eeee.......hhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeeee..eeeeeeeeee..eeeeeeeeehhhhhh.........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------NI_HGENASE_L_1            -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cc1 L  12 VKISIDPLTRVEGHLKIEVEVKDGKVVDAKCSGGMFRGFEQILRGRDPRDSSQIVQRICGVCPTAHCTASVMAQDDAFGVKVTTNGRITRNLIFGANYLQSHILHFYHLAALDYVKGPDVSPFVPRYANADLLTDRIKDGAKADATNTYGLNQYLKALEIRRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEYAARFKEVQKFVIEEYLPLIYTLGSVYTDLFETGIGWKNVIAFGVFPEDDDYKTFLLKPGVYIDGKDEEFDSKLVKEYVGHSFFDHSAPGGLHYSVGETNPNPDKPGAYSFVKAPRYKDKPCEVGPLARMWVQNPELSPVGQKLLKELYGIEAKKFRDLGDKAFSIMGRHVLRAEETWLTAVAVEKWLKQVQPGAETYVKSEIPDAAEGTGFTEAPRGALLHYLKIKDKKIENYQIVSATLWNANPRDDMGQRGPIEEALIGVPVPDIKNPVNVGRLVRSYDPxLGCAVH 498
                                    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|      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          492-SEC  


Chain S from PDB  Type:PROTEIN  Length:275
 aligned with PHSS_DESBA | P13063 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:278
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307        
           PHSS_DESBA    38 KKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKGHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETFTKPGCKAELGCKGPSTYADCAKRRWNNGINWCVENAVCIGCVEPDFPDGKSPFYVAE 315
               SCOP domains d1cc1s_ S: Nickel-iron hydrogenase, small subunit                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1cc1S01 S:6-202  [code=3.40.50.700, no name defined]                                                                                                                                                 1cc1S02 S:203-282 Cytochrome-c3 Hydrogenase, chain A, domain 2                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhh....hhhhhhhhheeeee.......hhhhhhhhhhhhhhhh....eeeee..ee.hhhhh..eee.---.......eehhhhhhhhhhhh.eeeeehhhhhhhhhhhh......eehhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh..............hhhhhh........hhhhhhh............hhhhh.hhhhh..hhhhhh......hhhhhh..........hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cc1 S   6 KKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGE---AKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETFTKPGCKAELGCKGPSTYADCAKRRWNNGINWCVENAVCIGCVEPDFPDGKSPFYVAE 283
                                    15        25        35        45        55        65        75        85       | - |     105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275        
                                                                                                                  93  97
   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  (0, 0)

(no "Pfam Domain" information available for 1CC1)

(-) Gene Ontology  (10, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (PHSL_DESBA | P13065)
molecular function
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0033748    hydrogenase (acceptor) activity    Catalysis of the reaction: H2 + A = AH2.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain S   (PHSS_DESBA | P13063)
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:0033748    hydrogenase (acceptor) activity    Catalysis of the reaction: H2 + A = AH2.
    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.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHSS_DESBA | P13063: 4kl8 4kn9 4ko1 4ko2 4ko3 4ko4

(-) Related Entries Specified in the PDB File

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