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(-) Description

Title :  BEST MODEL OF THE ELECTRON TRANSFER COMPLEX BETWEEN CYTOCHROME C3 AND [FE]-HYDROGENASE
 
Authors :  L. Elantak, X. Morelli, O. Bornet, C. Hatchikian, M. Czjzek, A. Dolla, F. Guerlesquin
Date :  28 Mar 02  (Deposition) - 31 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR; THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,D,E
Keywords :  Oxidoreductase, Electron Transfer Complex, Hydrogenase, Multiheme Cytochrome, Nmr, Soft Docking, Oxidoreductase Electron Transport, 4Fe-4S, Iron-Sulfur, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Elantak, X. Morelli, O. Bornet, C. Hatchikian, M. Czjzek, A. Dolla, F. Guerlesquin
The Cytochrome C(3)-[Fe]-Hydrogenase Electron-Transfer Complex: Structural Model By Nmr Restrained Docking
Febs Lett. V. 548 1 2003
PubMed-ID: 12885397  |  Reference-DOI: 10.1016/S0014-5793(03)00718-X

(-) Compounds

Molecule 1 - PERIPLASMIC [FE] HYDROGENASE LARGE SUBUNIT
    Chains: A
    EC Number: 1.18.99.1
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH
 
Molecule 2 - PERIPLASMIC [FE] HYDROGENASE SMALL SUBUNIT
    Chains: D
    EC Number: 1.18.99.1
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH
 
Molecule 3 - CYTOCHROME C3
    Chains: E
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 882
    Strain: HILDENBOROUGH

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Theoretical Model (6, 14)
No.NameCountTypeFull Name
1CMO2Ligand/IonCARBON MONOXIDE
2CYN2Ligand/IonCYANIDE ION
3FE22Ligand/IonFE (II) ION
4HEC4Ligand/IonHEME C
5PDT1Ligand/Ion1,3-PROPANEDITHIOL
6SF43Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (14, 14)

Theoretical Model (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPDT A:4 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , MET A:232BINDING SITE FOR RESIDUE FE2 A 5
02AC2SOFTWAREPDT A:4 , FE2 A:5 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , MET A:232BINDING SITE FOR RESIDUE FE2 A 6
03AC3SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:8 , CMO A:9 , CMO A:10 , PRO A:203 , ILE A:204 , MET A:232BINDING SITE FOR RESIDUE CYN A 7
04AC4SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CMO A:9 , CMO A:10 , ALA A:107 , PRO A:108 , ALA A:109 , MET A:232BINDING SITE FOR RESIDUE CYN A 8
05AC5SOFTWARELYS A:34 , CYS A:35 , ILE A:36 , CYS A:38 , ASP A:39 , CYS A:41 , SER A:42 , HIS A:58 , HIS A:75 , CYS A:76 , ILE A:81 , HEC E:109BINDING SITE FOR RESIDUE SF4 A 1
06AC6SOFTWARETYR A:44 , CYS A:45 , ILE A:50 , ALA A:65 , CYS A:66 , ILE A:67 , CYS A:69 , GLY A:70 , CYS A:72BINDING SITE FOR RESIDUE SF4 A 2
07AC7SOFTWARECYS A:69 , CYS A:179 , PRO A:180 , CYS A:234 , MET A:376 , ALA A:377 , CYS A:378 , CYS A:382 , GLY A:385 , GLY A:386BINDING SITE FOR RESIDUE SF4 A 3
08AC8SOFTWAREFE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , CMO A:10 , PRO A:203 , PHE A:296 , GLY A:297 , MET A:376 , CYS A:382BINDING SITE FOR RESIDUE PDT A 4
09AC9SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:10 , MET A:232 , PRO A:233 , LYS A:237BINDING SITE FOR RESIDUE CMO A 9
10BC1SOFTWAREPDT A:4 , FE2 A:5 , FE2 A:6 , CYN A:7 , CYN A:8 , CMO A:9 , PRO A:108 , THR A:145 , MET A:232BINDING SITE FOR RESIDUE CMO A 10
11BC2SOFTWARESF4 A:1 , ILE A:36 , CYS A:38 , MET A:54 , MET E:11 , GLU E:12 , ALA E:13 , THR E:14 , LYS E:15 , GLN E:16 , VAL E:18 , TYR E:65 , HIS E:70 , CYS E:79 , VAL E:80 , LEU E:97 , CYS E:100 , CYS E:105 , HIS E:106BINDING SITE FOR RESIDUE HEC E 109
12BC3SOFTWAREHIS E:34 , HIS E:35 , PRO E:36 , VAL E:37 , ASN E:38 , ASP E:42 , CYS E:46 , THR E:48 , CYS E:51 , HIS E:52 , SER E:61 , ALA E:62 , HIS E:67 , VAL E:68 , THR E:74 , LYS E:75 , PHE E:76BINDING SITE FOR RESIDUE HEC E 110
13BC4SOFTWAREPRO E:2 , LYS E:3 , ALA E:4 , PHE E:20 , HIS E:22 , HIS E:25 , LYS E:26 , CYS E:30 , CYS E:33 , HIS E:34 , ARG E:44 , LYS E:45 , CYS E:46 , GLY E:47 , HEC E:112BINDING SITE FOR RESIDUE HEC E 111
14BC5SOFTWAREVAL E:19 , PHE E:20 , ASN E:21 , SER E:23 , THR E:24 , HIS E:25 , CYS E:33 , MET E:69 , CYS E:79 , CYS E:82 , HIS E:83 , LYS E:104 , CYS E:105 , HEC E:111BINDING SITE FOR RESIDUE HEC E 112

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GX7)

(-) Cis Peptide Bonds  (2, 2)

Theoretical Model
No.Residues
1Leu A:172 -Pro A:173
2Leu D:108 -Pro D:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GX7)

(-) PROSITE Motifs  (3, 4)

Theoretical Model (3, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
14FE4S_FER_2PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.PHFL_DESVH26-57
59-86		  1-
A:59-86
24FE4S_FER_1PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.PHFL_DESVH35-46
66-77		  2A:35-46
A:66-77
3MULTIHEME_CYTCPS51008 Multiheme cytochrome c family profile.CYC3_DESVH47-110  1E:25-88

(-) Exons   (0, 0)

(no "Exon" information available for 1GX7)

(-) Sequences/Alignments

Theoretical Model
   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:371
 aligned with PHFL_DESVH | P07598 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:371
                                    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 
           PHFL_DESVH    27 FVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEA 397
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.........hhhhhh...................................eee...hhhhhhhhhhh...eeeee.hhhhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh........ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhh.............eeehhhhhhhhhhhh..hhhhh......................hhhhhhhhhhhh.....................eeeeeee....eeeeeee.hhhhhhhhhhhhhh......eeee.....hhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 4FE4S_FER_2  PDB: -            -4FE4S_FER_2  PDB: A:59-86   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------4FE4S_FER_1 -------------------4FE4S_FER_1 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gx7 A  27 FVQIDEAKCIGCDTCSQYCPTAAIFGEMGEPHSIPHIEACINCGQCLTHCPENAIYEAQSWVPEVEKKLKDGKVKCIAMPAPAVRYALGDAFGMPVGSVTTGKMLAALQKLGFAHCWDTEFTADVTIWEEGSEFVERLTKKSDMPLPQFTSCCPGWQKYAETYYPELLPHFSTCKSPIGMNGALAKTYGAERMKYDPKQVYTVSIMPCIAKKYEGLRPELKSSGMRDIDATLTTRELAYMIKKAGIDFAKLPDGKRDSLMGESTGGATIFGVTGGVMEAALRFAYEAVTGKKPDSWDFKAVRGLDGIKEATVNVGGTDVKVAVVHGAKRFKQVCDDVKAGKSPYHFIEYMACPGGCVCGGGQPVMPGVLEA 397
                                    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 


Chain D from PDB  Type:PROTEIN  Length:88
 aligned with PHFS_DESVH | P07603 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:88
                                    45        55        65        75        85        95       105       115        
           PHFS_DESVH    36 VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE 123
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhh........hhhhhh........hhhhhh.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 1gx7 D  36 VKQIKDYMLDRINGVYGADAKFPVRASQDNTQVKALYKSYLEKPLGHKSHDLLHTHWFDKSKGVKELTTAGKLPNPRASEFEGPYPYE 123
                                    45        55        65        75        85        95       105       115        


Chain E from PDB  Type:PROTEIN  Length:107
 aligned with CYC3_DESVH | P00131 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:107
                                    32        42        52        62        72        82        92       102       112       122       
           CYC3_DESVH    23 APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 129
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee......eee...........................................hhhhhhhh......hhhhhhhhhhh..hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------MULTIHEME_CYTC  PDB: E:25-88 UniProt: 47-110                    ------------------- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1gx7 E   1 APKAPADGLKMEATKQPVVFNHSTHKSVKCGDCHHPVNGKEDYRKCGTAGCHDSMDKKDKSAKGYYHVMHDKNTKFKSCVGCHVEVAGADAAKKKDLTGCKKSKCHE 107
                                    10        20        30        40        50        60        70        80        90       100
   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  (0, 0)

(no "SCOP Domain" information available for 1GX7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1GX7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GX7)

(-) Gene Ontology  (11, 22)

Theoretical Model(hide GO term definitions)
Chain A   (PHFL_DESVH | P07598)
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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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: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 D   (PHFS_DESVH | P07603)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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: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 E   (CYC3_DESVH | P00131)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009061    anaerobic respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.
    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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  PHFL_DESVH | P07598
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  PHFS_DESVH | P07603
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYC3_DESVH | P00131: 1a2i 1mdv 2bpn 2cth 2cym
        PHFL_DESVH | P07598: 1e08 1hfe
        PHFS_DESVH | P07603: 1e08 1hfe

(-) Related Entries Specified in the PDB File

1a2i SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS ( HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES
1hfe 1.6 A RESOLUTION STRUCTURE OF THE FE- ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS
1mdv KEY ROLE OF PHENYLALANINE 20 IN CYTOCHROME C3: STRUCTURE, STABILITY AND FUNCTION STUDIES
2cth CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH
2cym CYTOCHROME C3