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(-) Description

Title :  MEMBRANE-BOUND RESPIRATORY [NIFE] HYDROGENASE FROM HYDROGENOVIBRIO MARINUS IN A FERRICYANIDE-OXIDIZED CONDITION
 
Authors :  Y. Shomura, K. S. Yoon, H. Nishihara, Y. Higuchi
Date :  20 May 11  (Deposition) - 12 Oct 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Oxidoreductase, Membrane-Bound Ni-Fe Hydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Shomura, K. S. Yoon, H. Nishihara, Y. Higuchi
Structural Basis For A [4Fe-3S] Cluster In The Oxygen-Tolerant Membrane-Bound [Nife]-Hydrogenase
Nature V. 479 253 2011
PubMed-ID: 22002607  |  Reference-DOI: 10.1038/NATURE10504

(-) Compounds

Molecule 1 - MEMBRANE-BOUND HYDROGENASE LARGE SUBUNIT
    Chains: A, C
    EC Number: 1.12.5.1
    Organism Scientific: HYDROGENOVIBRIO MARINUS
    Organism Taxid: 28885
    Strain: MH-110
    Synonym: MEMBRANE-BOUND RESPIRATORY NI-FE HYDROGENASE LARGE SUBUNIT
 
Molecule 2 - MEMBRANE-BOUND HYDROGENASE SMALL SUBUNIT
    Chains: B, D
    EC Number: 1.12.5.1
    Fragment: UNP RESIDUES 41-323
    Organism Scientific: HYDROGENOVIBRIO MARINUS
    Organism Taxid: 28885
    Strain: MH-110
    Synonym: MEMBRANE-BOUND RESPIRATORY NI-FE HYDROGENASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 32)

Asymmetric/Biological Unit (10, 32)
No.NameCountTypeFull Name
13NI2Ligand/IonNICKEL (III) ION
2CMO2Ligand/IonCARBON MONOXIDE
3CYN4Ligand/IonCYANIDE ION
4F3S2Ligand/IonFE3-S4 CLUSTER
5FE22Ligand/IonFE (II) ION
6GOL4Ligand/IonGLYCEROL
7MG2Ligand/IonMAGNESIUM ION
8O10Ligand/IonOXYGEN ATOM
9SF32Ligand/IonFE4-S3 CLUSTER
10SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:79 , CYS A:593 , 3NI A:602 , CMO A:603 , CYN A:604 , CYN A:605 , O A:606 , O A:609BINDING SITE FOR RESIDUE FE2 A 601
02AC2SOFTWARECYS A:76 , CYS A:79 , CYS A:590 , CYS A:593 , FE2 A:601 , O A:606 , O A:607 , O A:608 , O A:609 , O A:610BINDING SITE FOR RESIDUE 3NI A 602
03AC3SOFTWARECYS A:79 , CYS A:82 , HIS A:83 , LEU A:526 , VAL A:544 , PRO A:545 , CYS A:593 , FE2 A:601 , CYN A:604 , CYN A:605BINDING SITE FOR RESIDUE CMO A 603
04AC4SOFTWARECYS A:79 , ALA A:521 , PRO A:522 , ARG A:523 , FE2 A:601 , CMO A:603 , CYN A:605 , O A:606BINDING SITE FOR RESIDUE CYN A 604
05AC5SOFTWAREARG A:523 , VAL A:544 , PRO A:545 , THR A:546 , CYS A:593 , FE2 A:601 , CMO A:603 , CYN A:604 , O A:606BINDING SITE FOR RESIDUE CYN A 605
06AC6SOFTWARECYS A:79 , ARG A:523 , CYS A:590 , CYS A:593 , FE2 A:601 , 3NI A:602 , CYN A:604 , CYN A:605 , O A:607 , O A:609 , O A:610BINDING SITE FOR RESIDUE O A 606
07AC7SOFTWARECYS A:76 , CYS A:590 , ALA A:592 , CYS A:593 , 3NI A:602 , O A:606 , O A:608 , O A:609 , O A:610BINDING SITE FOR RESIDUE O A 607
08AC8SOFTWAREGLU A:28 , CYS A:76 , CYS A:590 , LEU A:591 , ALA A:592 , CYS A:593 , 3NI A:602 , O A:607 , O A:610BINDING SITE FOR RESIDUE O A 608
09AC9SOFTWARECYS A:76 , CYS A:79 , CYS A:590 , CYS A:593 , FE2 A:601 , 3NI A:602 , O A:606 , O A:607 , O A:610BINDING SITE FOR RESIDUE O A 609
10BC1SOFTWARECYS A:76 , CYS A:79 , CYS A:590 , CYS A:593 , 3NI A:602 , O A:606 , O A:607 , O A:608 , O A:609BINDING SITE FOR RESIDUE O A 610
11BC2SOFTWARELYS A:310 , GLN A:319 , ASP A:482 , HOH A:851 , HOH A:1630BINDING SITE FOR RESIDUE GOL A 702
12BC3SOFTWAREILE A:242 , ASN A:243 , ILE A:244 , ASP A:245 , GLY A:246 , SER A:496 , HOH A:1055 , HOH A:1139 , ARG B:220BINDING SITE FOR RESIDUE GOL A 703
13BC4SOFTWAREGLU A:57 , CYS A:542 , HIS A:596 , HOH A:746 , HOH A:764 , HOH A:795BINDING SITE FOR RESIDUE MG A 701
14BC5SOFTWARECYS B:23 , THR B:24 , CYS B:25 , CYS B:26 , GLU B:82 , SER B:120 , CYS B:121 , CYS B:126 , GLY B:157 , CYS B:158BINDING SITE FOR RESIDUE SF3 B 301
15BC6SOFTWARELYS A:227 , THR B:235 , ASN B:237 , CYS B:239 , TRP B:244 , PRO B:251 , CYS B:258 , ILE B:259 , CYS B:261BINDING SITE FOR RESIDUE F3S B 308
16BC7SOFTWAREHIS B:196 , CYS B:199 , ARG B:202 , CYS B:224 , LEU B:225 , CYS B:230BINDING SITE FOR RESIDUE SF4 B 309
17BC8SOFTWAREGLU C:57 , CYS C:542 , HIS C:596 , HOH C:699 , HOH C:757 , HOH C:758BINDING SITE FOR RESIDUE MG C 701
18BC9SOFTWARECYS C:79 , CYS C:593 , 3NI C:602 , CMO C:603 , CYN C:604 , CYN C:605 , O C:606 , O C:609BINDING SITE FOR RESIDUE FE2 C 601
19CC1SOFTWARECYS C:76 , CYS C:79 , CYS C:590 , CYS C:593 , FE2 C:601 , O C:606 , O C:607 , O C:608 , O C:609 , O C:610BINDING SITE FOR RESIDUE 3NI C 602
20CC2SOFTWARECYS C:79 , CYS C:82 , HIS C:83 , LEU C:526 , VAL C:544 , PRO C:545 , CYS C:593 , FE2 C:601 , CYN C:604 , CYN C:605BINDING SITE FOR RESIDUE CMO C 603
21CC3SOFTWARECYS C:79 , ALA C:521 , PRO C:522 , ARG C:523 , FE2 C:601 , CMO C:603 , CYN C:605 , O C:606BINDING SITE FOR RESIDUE CYN C 604
22CC4SOFTWAREVAL C:544 , PRO C:545 , THR C:546 , CYS C:593 , FE2 C:601 , CMO C:603 , CYN C:604 , O C:606BINDING SITE FOR RESIDUE CYN C 605
23CC5SOFTWARECYS C:79 , ARG C:523 , CYS C:590 , CYS C:593 , FE2 C:601 , 3NI C:602 , CYN C:604 , CYN C:605 , O C:607 , O C:609 , O C:610BINDING SITE FOR RESIDUE O C 606
24CC6SOFTWARECYS C:76 , CYS C:590 , ALA C:592 , CYS C:593 , 3NI C:602 , O C:606 , O C:608 , O C:609 , O C:610BINDING SITE FOR RESIDUE O C 607
25CC7SOFTWAREGLU C:28 , CYS C:76 , CYS C:590 , LEU C:591 , ALA C:592 , CYS C:593 , 3NI C:602 , O C:607 , O C:610BINDING SITE FOR RESIDUE O C 608
26CC8SOFTWARECYS C:76 , CYS C:79 , CYS C:590 , CYS C:593 , FE2 C:601 , 3NI C:602 , O C:606 , O C:607 , O C:610BINDING SITE FOR RESIDUE O C 609
27CC9SOFTWARECYS C:76 , CYS C:79 , CYS C:590 , CYS C:593 , 3NI C:602 , O C:606 , O C:607 , O C:608 , O C:609BINDING SITE FOR RESIDUE O C 610
28DC1SOFTWARELYS C:310 , GLN C:319 , TYR C:475 , ASP C:482 , HOH C:789BINDING SITE FOR RESIDUE GOL C 702
29DC2SOFTWAREILE C:242 , ASN C:243 , ILE C:244 , ASP C:245 , SER C:496 , HOH C:1514 , ARG D:220BINDING SITE FOR RESIDUE GOL C 703
30DC3SOFTWARECYS D:23 , THR D:24 , CYS D:25 , CYS D:26 , GLU D:82 , SER D:120 , CYS D:121 , CYS D:126 , GLY D:157 , CYS D:158BINDING SITE FOR RESIDUE SF3 D 301
31DC4SOFTWARELYS C:227 , THR D:235 , ASN D:237 , CYS D:239 , TRP D:244 , PRO D:251 , CYS D:258 , ILE D:259 , CYS D:261BINDING SITE FOR RESIDUE F3S D 308
32DC5SOFTWAREHIS D:196 , CYS D:199 , ARG D:202 , CYS D:224 , LEU D:225 , CYS D:230BINDING SITE FOR RESIDUE SF4 D 309

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:76 -A:590
2C:76 -C:590

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Asp A:22 -Pro A:23
2Asn A:228 -Pro A:229
3His B:35 -Pro B:36
4Lys B:131 -Pro B:132
5Cys B:158 -Pro B:159
6Asp C:22 -Pro C:23
7Asn C:228 -Pro C:229
8His D:35 -Pro D:36
9Lys D:131 -Pro D:132
10Cys D:158 -Pro D:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AYY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AYY)

(-) Exons   (0, 0)

(no "Exon" information available for 3AYY)

(-) 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:595
 aligned with F2Z6J6_HYDMR | F2Z6J6 from UniProtKB/TrEMBL  Length:611

    Alignment length:595
                                    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       591     
         F2Z6J6_HYDMR     2 SVLNTPNHYKMDNSGRRVVIDPVTRIEGHMRCEVNVDENNVIQNAVSTGTMWRGLEVILRGRDPRDAWAFVERICGVCTGCHALASVRAVEDALDIKIPHNATLIREIMAKTLQIHDHIVHFYHLHALDWVNPVNALKADPQATSELQKLVSPHHPMSSPGYFKDIQIRIQKFVDSGQLGIFKNGYWSNPAYKLSPEADLMAVTHYLEALDFQKEIVKIHAIFGGKNPHPNYMVGGVPCAINIDGDMAAGAPINMERLNFVKSLIEQGRTFNTNVYVPDVIAIAAFYRDWLYGGGLSATNVMDYGAYPKTPYDKSTDQLPGGAIINGDWGKIHPVDPRDPEQVQEFVTHSWYKYPDETKGLHPWDGITEPNYELGSKTKGSRTNIIEIDESAKYSWIKSPRWRGHAVEVGPLARYILAYAQGVEYVKTQVHTSLNRFNAVCRLLDPNHKDITDLKAFLGSTIGRTLARALESEYCGDMMLDDFNQLISNIKNGDSSTANTDKWDPSSWPEHAKGVGTVAAPRGALAHWIVIEKGKIKNYQCVVPTTWNGSPRDPKGNIGAFEASLMGTPMERPDEPVEVLRTLHSFDPCLACSTH 596
               SCOP domains d3ayya_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...eeeee.........eeeeeee.....eeeeeeee....hhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.eee..eee....hhh.eee..eee..................eeee...............hhhhh............eee..eeee...........eeee.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ayy A   2 SVLNTPNHYKMDNSGRRVVIDPVTRIEGHMRCEVNVDENNVIQNAVSTGTMWRGLEVILRGRDPRDAWAFVERICGVCTGCHALASVRAVEDALDIKIPHNATLIREIMAKTLQIHDHIVHFYHLHALDWVNPVNALKADPQATSELQKLVSPHHPMSSPGYFKDIQIRIQKFVDSGQLGIFKNGYWSNPAYKLSPEADLMAVTHYLEALDFQKEIVKIHAIFGGKNPHPNYMVGGVPCAINIDGDMAAGAPINMERLNFVKSLIEQGRTFNTNVYVPDVIAIAAFYRDWLYGGGLSATNVMDYGAYPKTPYDKSTDQLPGGAIINGDWGKIHPVDPRDPEQVQEFVTHSWYKYPDETKGLHPWDGITEPNYELGSKTKGSRTNIIEIDESAKYSWIKSPRWRGHAVEVGPLARYILAYAQGVEYVKTQVHTSLNRFNAVCRLLDPNHKDITDLKAFLGSTIGRTLARALESEYCGDMMLDDFNQLISNIKNGDSSTANTDKWDPSSWPEHAKGVGTVAAPRGALAHWIVIEKGKIKNYQCVVPTTWNGSPRDPKGNIGAFEASLMGTPMERPDEPVEVLRTLHSFDPCLACSTH 596
                                    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       591     


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with F2Z6J5_HYDMR | F2Z6J5 from UniProtKB/TrEMBL  Length:361

    Alignment length:273
                                    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       320   
         F2Z6J5_HYDMR    51 PRTPVIWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAASGHAAEAILDEIKEKYKGNYILAVEGNPPLNQDGMSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEEWDDEGARKGYCLYKVGCKGPTTYNACSTVRWNGGTSFPIQSGHGCIGCSEDGFWDKGSFYSRDTEMNAFG 323
               SCOP domains d3ayyb_ B: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhh....hhhhhhhhheeeeee......hhhhhhhhhhhhhhhh....eeeee.....hhhhh..ee..eehhhhhhhhhhhh.eeeeehhhhhh.hhhhh........hhhhhhh......eeee.....hhhhhhhhhhhhhhhh..........hhhhhh.hhhhh..hhhhhhh........hhhhhh...hhhhh.hhhhh.............................hhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ayy B  11 PRTPVIWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAASGHAAEAILDEIKEKYKGNYILAVEGNPPLNQDGMSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEEWDDEGARKGYCLYKVGCKGPTTYNACSTVRWNGGTSFPIQSGHGCIGCSEDGFWDKGSFYSRDTEMNAFG 283
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280   


Chain C from PDB  Type:PROTEIN  Length:595
 aligned with F2Z6J6_HYDMR | F2Z6J6 from UniProtKB/TrEMBL  Length:611

    Alignment length:595
                                    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       591     
         F2Z6J6_HYDMR     2 SVLNTPNHYKMDNSGRRVVIDPVTRIEGHMRCEVNVDENNVIQNAVSTGTMWRGLEVILRGRDPRDAWAFVERICGVCTGCHALASVRAVEDALDIKIPHNATLIREIMAKTLQIHDHIVHFYHLHALDWVNPVNALKADPQATSELQKLVSPHHPMSSPGYFKDIQIRIQKFVDSGQLGIFKNGYWSNPAYKLSPEADLMAVTHYLEALDFQKEIVKIHAIFGGKNPHPNYMVGGVPCAINIDGDMAAGAPINMERLNFVKSLIEQGRTFNTNVYVPDVIAIAAFYRDWLYGGGLSATNVMDYGAYPKTPYDKSTDQLPGGAIINGDWGKIHPVDPRDPEQVQEFVTHSWYKYPDETKGLHPWDGITEPNYELGSKTKGSRTNIIEIDESAKYSWIKSPRWRGHAVEVGPLARYILAYAQGVEYVKTQVHTSLNRFNAVCRLLDPNHKDITDLKAFLGSTIGRTLARALESEYCGDMMLDDFNQLISNIKNGDSSTANTDKWDPSSWPEHAKGVGTVAAPRGALAHWIVIEKGKIKNYQCVVPTTWNGSPRDPKGNIGAFEASLMGTPMERPDEPVEVLRTLHSFDPCLACSTH 596
               SCOP domains d3ayyc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee...eeeee.........eeeeeee.....eeeeeeee....hhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eee..eee....hhh.eee..eee..................eeee...............hhhhh............eee..eeee...........eeee.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ayy C   2 SVLNTPNHYKMDNSGRRVVIDPVTRIEGHMRCEVNVDENNVIQNAVSTGTMWRGLEVILRGRDPRDAWAFVERICGVCTGCHALASVRAVEDALDIKIPHNATLIREIMAKTLQIHDHIVHFYHLHALDWVNPVNALKADPQATSELQKLVSPHHPMSSPGYFKDIQIRIQKFVDSGQLGIFKNGYWSNPAYKLSPEADLMAVTHYLEALDFQKEIVKIHAIFGGKNPHPNYMVGGVPCAINIDGDMAAGAPINMERLNFVKSLIEQGRTFNTNVYVPDVIAIAAFYRDWLYGGGLSATNVMDYGAYPKTPYDKSTDQLPGGAIINGDWGKIHPVDPRDPEQVQEFVTHSWYKYPDETKGLHPWDGITEPNYELGSKTKGSRTNIIEIDESAKYSWIKSPRWRGHAVEVGPLARYILAYAQGVEYVKTQVHTSLNRFNAVCRLLDPNHKDITDLKAFLGSTIGRTLARALESEYCGDMMLDDFNQLISNIKNGDSSTANTDKWDPSSWPEHAKGVGTVAAPRGALAHWIVIEKGKIKNYQCVVPTTWNGSPRDPKGNIGAFEASLMGTPMERPDEPVEVLRTLHSFDPCLACSTH 596
                                    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       591     


Chain D from PDB  Type:PROTEIN  Length:267
 aligned with F2Z6J5_HYDMR | F2Z6J5 from UniProtKB/TrEMBL  Length:361

    Alignment length:267
                                    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       
         F2Z6J5_HYDMR    51 PRTPVIWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAASGHAAEAILDEIKEKYKGNYILAVEGNPPLNQDGMSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEEWDDEGARKGYCLYKVGCKGPTTYNACSTVRWNGGTSFPIQSGHGCIGCSEDGFWDKGSFYSRDT 317
               SCOP domains d3ayyd_ D: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhh....hhhhhhhhheeeeee......hhhhhhhhhhhhhhhh...eeeeee.....hhhhh..ee..eehhhhhhhhhhheeeeeeehhhhhhhhhhhh........hhhhhhh......eeee.....hhhhhhhhhhhhhhhh..........hhhhhh.hhhhh..hhhhhhh........hhhhhh...hhhhh.hhhhh.............................hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ayy D  11 PRTPVIWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAASGHAAEAILDEIKEKYKGNYILAVEGNPPLNQDGMSCIIGGRPFSEQLKRMADDAKAIISWGSCASWGCVQAAKPNPTQATPVHKFLGGGYDKPIIKVPGCPPIAEVMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEEWDDEGARKGYCLYKVGCKGPTTYNACSTVRWNGGTSFPIQSGHGCIGCSEDGFWDKGSFYSRDT 277
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AYY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AYY)

(-) Gene Ontology  (9, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (F2Z6J6_HYDMR | F2Z6J6)
molecular function
    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.

Chain B,D   (F2Z6J5_HYDMR | F2Z6J5)
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.
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.

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 Related Entries

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

UniProtKB/TrEMBL
        F2Z6J5_HYDMR | F2Z6J5: 3ayx 3ayz
        F2Z6J6_HYDMR | F2Z6J6: 3ayx 3ayz

(-) Related Entries Specified in the PDB File

3ayx MEMBRANE-BOUND RESPIRATORY [NIFE] HYDROGENASE FROM HYDROGENOVIBRIO MARINUS IN AN H2-REDUCED CONDITION
3ayz MEMBRANE-BOUND RESPIRATORY [NIFE] HYDROGENASE FROM HYDROGENOVIBRIO MARINUS IN AN AIR-OXIDIZED CONDITION