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(-) Description

Title :  STRUCTURE OF THE UNREADY OXIDIZED FORM OF [NIFE] HYDROGENASE
 
Authors :  A. Volbeda, L. Martin, C. Cavazza, M. Matho, B. W. Faber, W. Roseboom, S. P. Albracht, E. Garcin, M. Rousset, J. C. Fontecilla-Camps
Date :  01 Feb 05  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,H,I
Biol. Unit 1:  A,H  (1x)
Biol. Unit 2:  B,I  (1x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Volbeda, L. Martin, C. Cavazza, M. Matho, B. W. Faber, W. Roseboom, S. P. Albracht, E. Garcin, M. Rousset, J. C. Fontecilla-Camps
Structural Differences Between The Ready And Unready Oxidized States Of [Nife] Hydrogenases.
J. Biol. Inorg. Chem. V. 10 239 2005
PubMed-ID: 15803334  |  Reference-DOI: 10.1007/S00775-005-0632-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
    Cellular Location: PERIPLASM
    Chains: A, B
    EC Number: 1.12.2.1
    Organism Scientific: DESULFOVIBRIO GIGAS
    Organism Taxid: 879
    Strain: WILD TYPE
    Synonym: NIFE HYDROGENLYASE SMALL CHAIN
 
Molecule 2 - PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
    Cellular Location: PERIPLASM
    Chains: H, I
    EC Number: 1.12.2.1
    Organism Scientific: DESULFOVIBRIO GIGAS
    Organism Taxid: 879
    Strain: WILD TYPE
    Synonym: NIFE HYDROGENLYASE LARGE CHAIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHI
Biological Unit 1 (1x): A H 
Biological Unit 2 (1x):  B I

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 25)

Asymmetric Unit (8, 25)
No.NameCountTypeFull Name
1F3S2Ligand/IonFE3-S4 CLUSTER
2FCO2Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
3GOL7Ligand/IonGLYCEROL
4H2S4Ligand/IonHYDROSULFURIC ACID
5MG2Ligand/IonMAGNESIUM ION
6NI2Ligand/IonNICKEL (II) ION
7PER2Ligand/IonPEROXIDE ION
8SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (6, 13)
No.NameCountTypeFull Name
1F3S1Ligand/IonFE3-S4 CLUSTER
2FCO1Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
3GOL6Ligand/IonGLYCEROL
4H2S2Ligand/IonHYDROSULFURIC ACID
5MG-1Ligand/IonMAGNESIUM ION
6NI-1Ligand/IonNICKEL (II) ION
7PER1Ligand/IonPEROXIDE ION
8SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (6, 8)
No.NameCountTypeFull Name
1F3S1Ligand/IonFE3-S4 CLUSTER
2FCO1Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
3GOL1Ligand/IonGLYCEROL
4H2S2Ligand/IonHYDROSULFURIC ACID
5MG-1Ligand/IonMAGNESIUM ION
6NI-1Ligand/IonNICKEL (II) ION
7PER1Ligand/IonPEROXIDE ION
8SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS H:65 , CYS H:68 , CYS H:530 , CYS H:533 , FCO H:537 , PER H:539BINDING SITE FOR RESIDUE NI H 538
02AC2SOFTWARECYS I:65 , CYS I:68 , CYS I:530 , CYS I:533 , FCO I:537 , PER I:539BINDING SITE FOR RESIDUE NI I 538
03AC3SOFTWAREGLU H:46 , LEU H:482 , HIS H:536 , HOH H:5011 , HOH H:5012 , HOH H:5013BINDING SITE FOR RESIDUE MG H 540
04AC4SOFTWAREGLU I:46 , LEU I:482 , HIS I:536 , HOH I:5024 , HOH I:5025 , HOH I:5026BINDING SITE FOR RESIDUE MG I 540
05AC5SOFTWAREHIS A:185 , CYS A:188 , ARG A:190 , LEU A:191 , CYS A:213 , LEU A:214 , CYS A:219BINDING SITE FOR RESIDUE SF4 A 265
06AC6SOFTWARETHR A:224 , ASN A:226 , CYS A:228 , PHE A:233 , TRP A:238 , CYS A:246 , ILE A:247 , CYS A:249 , LYS H:216 , GLN H:221BINDING SITE FOR RESIDUE F3S A 266
07AC7SOFTWAREGLU A:16 , CYS A:17 , CYS A:20 , THR A:111 , CYS A:112 , GLY A:147 , CYS A:148 , PRO A:149 , ARG H:63BINDING SITE FOR RESIDUE SF4 A 267
08AC8SOFTWAREGLY A:117 , ASN A:253 , HOH A:1551BINDING SITE FOR RESIDUE H2S A 1268
09AC9SOFTWARECYS H:68 , VAL H:71 , HIS H:72 , ALA H:461 , PRO H:462 , ARG H:463 , LEU H:466 , PRO H:485 , SER H:486 , CYS H:533 , NI H:538 , PER H:539BINDING SITE FOR RESIDUE FCO H 537
10BC1SOFTWARECYS H:65 , CYS H:68 , ARG H:463 , CYS H:530 , CYS H:533 , FCO H:537 , NI H:538BINDING SITE FOR RESIDUE PER H 539
11BC2SOFTWAREARG H:55 , VAL H:225 , HOH H:5059BINDING SITE FOR RESIDUE H2S H 1541
12BC3SOFTWAREHIS B:185 , CYS B:188 , ARG B:190 , LEU B:191 , CYS B:213 , LEU B:214 , CYS B:219BINDING SITE FOR RESIDUE SF4 B 265
13BC4SOFTWAREASN B:226 , CYS B:228 , PHE B:233 , TRP B:238 , CYS B:246 , ILE B:247 , CYS B:249 , LYS I:216 , GLN I:221BINDING SITE FOR RESIDUE F3S B 266
14BC5SOFTWARECYS B:17 , CYS B:20 , GLY B:110 , THR B:111 , CYS B:112 , GLY B:147 , CYS B:148 , PRO B:149 , ARG I:63BINDING SITE FOR RESIDUE SF4 B 267
15BC6SOFTWARETYR B:115 , GLY B:117 , ASN B:253 , HOH B:291BINDING SITE FOR RESIDUE H2S B 2268
16BC7SOFTWARECYS I:68 , HIS I:72 , ALA I:461 , PRO I:462 , ARG I:463 , VAL I:484 , PRO I:485 , SER I:486 , CYS I:533 , NI I:538 , PER I:539BINDING SITE FOR RESIDUE FCO I 537
17BC8SOFTWARECYS I:68 , ARG I:463 , CYS I:530 , CYS I:533 , FCO I:537 , NI I:538BINDING SITE FOR RESIDUE PER I 539
18BC9SOFTWAREARG I:55 , VAL I:224 , VAL I:225 , HOH I:5061 , HOH I:5071BINDING SITE FOR RESIDUE H2S I 2541
19CC1SOFTWAREHIS A:54 , GLY A:88 , ARG A:90 , GOL A:1272 , HOH A:1562 , PHE B:194BINDING SITE FOR RESIDUE GOL A 1271
20CC2SOFTWAREGLU A:57 , LEU A:60 , HIS A:61 , ILE A:64 , ARG A:90 , GLU A:98 , GOL A:1271 , PHE B:194 , TYR B:215BINDING SITE FOR RESIDUE GOL A 1272
21CC3SOFTWARELYS A:102 , HOH A:1639 , HOH A:1642 , LEU B:257 , ALA B:264 , HOH B:313 , HOH B:328BINDING SITE FOR RESIDUE GOL A 1273
22CC4SOFTWAREALA A:208 , LYS A:209 , GLY A:211 , HOH A:1549 , HOH A:1655 , ASP H:232BINDING SITE FOR RESIDUE GOL A 1542
23CC5SOFTWAREGLY A:89 , GLY B:197 , HOH B:326 , HOH B:355 , GLU H:347 , PHE H:348 , HOH H:5136BINDING SITE FOR RESIDUE GOL H 1543
24CC6SOFTWAREVAL H:84 , ASN H:128 , ASP H:446 , TRP H:447 , GLN H:448 , HOH H:5021BINDING SITE FOR RESIDUE GOL H 1544
25CC7SOFTWAREALA B:208 , LYS B:209 , GLY B:211 , HOH B:375 , ASP I:232BINDING SITE FOR RESIDUE GOL B 2542

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YQ9)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asp A:29 -Pro A:30
2Lys A:122 -Pro A:123
3Cys A:148 -Pro A:149
4Ser A:259 -Pro A:260
5Asp H:12 -Pro H:13
6Asn H:217 -Pro H:218
7Asp B:29 -Pro B:30
8Lys B:122 -Pro B:123
9Cys B:148 -Pro B:149
10Ser B:259 -Pro B:260
11Asp I:12 -Pro I:13
12Asn I:217 -Pro I:218

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YQ9)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NI_HGENASE_L_1PS00507 Nickel-dependent hydrogenases large subunit signature 1.PHNL_DESGI43-68
 		  2H:43-68
I:43-68
2NI_HGENASE_L_2PS00508 Nickel-dependent hydrogenases large subunit signature 2.PHNL_DESGI527-536
 		  2H:527-536
I:527-536
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NI_HGENASE_L_1PS00507 Nickel-dependent hydrogenases large subunit signature 1.PHNL_DESGI43-68
 		  1H:43-68
-
2NI_HGENASE_L_2PS00508 Nickel-dependent hydrogenases large subunit signature 2.PHNL_DESGI527-536
 		  1H:527-536
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NI_HGENASE_L_1PS00507 Nickel-dependent hydrogenases large subunit signature 1.PHNL_DESGI43-68
 		  1-
I:43-68
2NI_HGENASE_L_2PS00508 Nickel-dependent hydrogenases large subunit signature 2.PHNL_DESGI527-536
 		  1-
I:527-536

(-) Exons   (0, 0)

(no "Exon" information available for 1YQ9)

(-) Sequences/Alignments

Asymmetric 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:261
 aligned with PHNS_DESGI | P12943 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:261
                                    37        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 
           PHNS_DESGI    28 KKRPSVVYLHNAECTGCSESLLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGRRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNFWDLYSPFYSA 288
               SCOP domains d1yq9a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1yq9A01 A:4-179  [code=3.40.50.700, no name defined]                                                                                                                            1yq9A02 A:180-264 Cytochrome-c3 Hydrogenase, chain A, domain 2                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhh....hhhhhhhhh.eeee........hhhhhhhhhhhh...eeeeee..ee.hhhh...ee..eehhhhhhhhhhhh.eeeeehhhhhhhhhhhh......eehhhhhhhhhh...eee.....hhhhhhhhhhhhhhh..........hhhhhh..hhhhh.hhhhhhhh.......hhhhhh...hhhhh.hhhhh..hhhhhh....................hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yq9 A   4 KKRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNFWDLYSPFYSA 264
                                    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 B from PDB  Type:PROTEIN  Length:260
 aligned with PHNS_DESGI | P12943 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:260
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
           PHNS_DESGI    29 KRPSVVYLHNAECTGCSESLLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGRRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNFWDLYSPFYSA 288
               SCOP domains d1yq9b_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1yq9B01 B:5-179  [code=3.40.50.700, no name defined]                                                                                                                           1yq9B02 B:180-264 Cytochrome-c3 Hydrogenase, chain A, domain 2                        CATH domains
           Pfam domains (1) ------------Oxidored_q6-1yq9B01 B:17-162                                                                                                                      ------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------Oxidored_q6-1yq9B02 B:17-162                                                                                                                      ------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...eeeeee....hhhhhhhhh....hhhhhhhhh.eeee........hhhhhhhhhhhh...eeeeee..ee.hhhh...ee..eehhhhhhhhhhhh.eeeeehhhhhhhhhhhh......eehhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh.........hhhhhh..hhhhh.hhhhhhhh.......hhhhhh...hhhhh.hhhhh..hhhhhh....................hhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yq9 B   5 KRPSVVYLHNAECTGCSESVLRTVDPYVDELILDVISMDYHETLMAGAGHAVEEALHEAIKGDFVCVIEGGIPMGDGGYWGKVGGRNMYDICAEVAPKAKAVIAIGTCATYGGVQAAKPNPTGTVGVNEALGKLGVKAINIAGCPPNPMNFVGTVVHLLTKGMPELDKQGRPVMFFGETVHDNCPRLKHFEAGEFATSFGSPEAKKGYCLYELGCKGPDTYNNCPKQLFNQVNWPVQAGHPCIACSEPNFWDLYSPFYSA 264
                                    14        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


Chain H from PDB  Type:PROTEIN  Length:530
 aligned with PHNL_DESGI | P12944 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:530
                                    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       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536
           PHNL_DESGI     7 NKIVVDPITRIEGHLRIEVEVEGGKIKNAWSMSTLFRGLEMILKGRDPRDAQHFTQRACGVCTYVHALASVRAVDNCVGVKIPENATLMRNLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQAKVKALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRPERIAEFRKLYKEVREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSRYTPQGVIWGNDLSKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTKPKWTEFHGEDRYSWMKAPRYKGEAFEVGPLASVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLGRTAARGIQCLTAAQEVEVWLDKLEANVKAGKDDLYTDWQYPTESQGVGFVNAPRGMLSHWIVQRGGKIENFQHVVPSTWNLGPRCAERKLSAVEQALIGTPIADPKRPVEILRTVHSYDPCIACGVH 536
               SCOP domains d1yq9h1 H:7-536 Nickel-iron hydrogenase, large subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1yq9H00 H:7-536 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeeeee..eeeeeeeee....hhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.........hhhhh....eee...........hhh.eeee............hhhhh.........hhhhh.....eeee.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------NI_HGENASE_L_1            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yq9 H   7 NKIVVDPITRIEGHLRIEVEVEGGKIKNAWSMSTLFRGLEMILKGRDPRDAQHFTQRACGVCTYVHALASVRAVDNCVGVKIPENATLMRNLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQAKVKALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRPERIAEFRKLYKEVREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSRYTPQGVIWGNDLSKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTKPKWTEFHGEDRYSWMKAPRYKGEAFEVGPLASVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLGRTAARGIQCLTAAQEVEVWLDKLEANVKAGKDDLYTDWQYPTESQGVGFVNAPRGMLSHWIVQRGGKIENFQLVVPSTWNLGPRCAEGKLSAVEQALIGTPIADPKRPVEILRTVHSYDPCIACGVH 536
                                    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       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536


Chain I from PDB  Type:PROTEIN  Length:530
 aligned with PHNL_DESGI | P12944 from UniProtKB/Swiss-Prot  Length:551

    Alignment length:530
                                    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       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536
           PHNL_DESGI     7 NKIVVDPITRIEGHLRIEVEVEGGKIKNAWSMSTLFRGLEMILKGRDPRDAQHFTQRACGVCTYVHALASVRAVDNCVGVKIPENATLMRNLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQAKVKALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRPERIAEFRKLYKEVREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSRYTPQGVIWGNDLSKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTKPKWTEFHGEDRYSWMKAPRYKGEAFEVGPLASVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLGRTAARGIQCLTAAQEVEVWLDKLEANVKAGKDDLYTDWQYPTESQGVGFVNAPRGMLSHWIVQRGGKIENFQHVVPSTWNLGPRCAERKLSAVEQALIGTPIADPKRPVEILRTVHSYDPCIACGVH 536
               SCOP domains d1yq9i_ I: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1yq9I00 I:7-536 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
           Pfam domains (1) ------------------------------------NiFeSe_Hases-1yq9I01 I:43-535                                                                                                                                                                                                                                                                                                                                                                                                                                                                                - Pfam domains (1)
           Pfam domains (2) ------------------------------------NiFeSe_Hases-1yq9I02 I:43-535                                                                                                                                                                                                                                                                                                                                                                                                                                                                                - Pfam domains (2)
         Sec.struct. author .eeee.........eeeeeeee..eeeeeeeee....hhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eee....hhh.eee..eee...........hhh.eeee............hhhhh.........hhhhh.....eeee.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------NI_HGENASE_L_1            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yq9 I   7 NKIVVDPITRIEGHLRIEVEVEGGKIKNAWSMSTLFRGLEMILKGRDPRDAQHFTQRACGVCTYVHALASVRAVDNCVGVKIPENATLMRNLTMGAQYMHDHLVHFYHLHALDWVNVANALNADPAKAARLANDLSPRKTTTESLKAVQAKVKALVESGQLGIFTNAYFLGGHPAYVLPAEVDLIATAHYLEALRVQVKAARAMAIFGAKNPHTQFTVVGGCTNYDSLRPERIAEFRKLYKEVREFIEQVYITDLLAVAGFYKNWAGIGKTSNFLTCGEFPTDEYDLNSRYTPQGVIWGNDLSKVDDFNPDLIEEHVKYSWYEGADAHHPYKGVTKPKWTEFHGEDRYSWMKAPRYKGEAFEVGPLASVLVAYAKKHEPTVKAVDLVLKTLGVGPEALFSTLGRTAARGIQCLTAAQEVEVWLDKLEANVKAGKDDLYTDWQYPTESQGVGFVNAPRGMLSHWIVQRGGKIENFQLVVPSTWNLGPRCAEGKLSAVEQALIGTPIADPKRPVEILRTVHSYDPCIACGVH 536
                                    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       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536
   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)
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 Classification and Annotation

(-) SCOP Domains  (3, 4)

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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (11, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PHNS_DESGI | P12943)
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:0047806    cytochrome-c3 hydrogenase activity    Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
    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.
    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 H,I   (PHNL_DESGI | P12944)
molecular function
    GO:0047806    cytochrome-c3 hydrogenase activity    Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    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).

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  PHNS_DESGI | P12943
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 Related Entries

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

UniProtKB/Swiss-Prot
        PHNL_DESGI | P12944: 1frv 2frv
        PHNS_DESGI | P12943: 1frv 2frv

(-) Related Entries Specified in the PDB File

2frv SAME PROTEIN REFINED AT 2.54 ANGSTROM RESOLUTION