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(-) Description

Title :  A NOVEL IRON CENTRE IN THE SPLIT-SORET CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774
 
Authors :  I. A. Abreu, A. I. Lourenco, A. V. Xavier, J. Legall, A. V. Coelho, P. M. Matias, D. M. Pinto, M. A. Carrondo, M. Teixeira, L. M. Saraiva
Date :  30 Jul 02  (Deposition) - 20 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cytochrome, Dimeric Di-Heme Cytochrome, Stacked Heme Arrangement, Novel Fold, Novel Iron-Sulfur Centre, Electron Transport, Sulfate Respiration (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. A. Abreu, A. I. Lourenco, A. V. Xavier, J. Legall, A. V. Coelho, P. M. Matias, D. M. Pinto, M. Armenia Carrondo, M. Teixeira, L. M. Saraiva
A Novel Iron Centre In The Split-Soret Cytochrome C From Desulfovibrio Desulfuricans Atcc 27774
J. Biol. Inorg. Chem. V. 8 360 2003
PubMed-ID: 12589573  |  Reference-DOI: 10.1007/S00775-002-0426-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPLIT-SORET CYTOCHROME C
    Atcc27774
    ChainsA, B, C, D
    Organism ScientificDESULFOVIBRIO DESULFURICANS
    Organism Taxid876
    SynonymDIMERIC DI-HEME SPLIT-SORET CYTOCHROME C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1HEC8Ligand/IonHEME C
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1HEC4Ligand/IonHEME C
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1HEC4Ligand/IonHEME C

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:208 , CYS A:209 , CYS A:212 , HIS A:213 , TRP A:222 , HIS A:233 , HEC A:1249 , LYS B:242 , PHE B:243 , HIS B:246 , PRO B:247BINDING SITE FOR RESIDUE HEC A1248
2AC2SOFTWARECYS A:209 , HIS A:213 , GLY A:225 , MET A:227 , ASP A:228 , CYS A:229 , CYS A:232 , HIS A:233 , HEC A:1248 , HIS B:148 , ILE B:149 , SER B:152 , LYS B:153 , TYR B:156 , PRO B:231 , ALA B:238 , HEC B:1249BINDING SITE FOR RESIDUE HEC A1249
3AC3SOFTWARETYR A:156 , ALA A:237 , ALA A:238 , LYS A:242 , HIS A:246 , PRO A:247 , CYS B:209 , CYS B:212 , HIS B:213 , ALA B:220 , HIS B:233 , HEC B:1249BINDING SITE FOR RESIDUE HEC B1248
4AC4SOFTWAREHIS A:148 , ILE A:149 , SER A:152 , LYS A:153 , TYR A:156 , ALA A:238 , HEC A:1249 , CYS B:209 , HIS B:213 , MET B:214 , GLY B:225 , MET B:227 , ASP B:228 , CYS B:229 , CYS B:232 , HIS B:233 , HEC B:1248BINDING SITE FOR RESIDUE HEC B1249
5AC5SOFTWARECYS C:209 , HIS C:213 , MET C:214 , GLY C:225 , MET C:227 , ASP C:228 , CYS C:229 , CYS C:232 , HIS C:233 , HIS D:148 , ILE D:149 , SER D:152 , LYS D:153 , TYR D:156 , PRO D:231 , ALA D:238 , HEC D:1248 , HEC D:1250BINDING SITE FOR RESIDUE HEC C1248
6AC6SOFTWARELYS B:23 , LEU B:24 , ASP B:25 , CYS C:209 , CYS C:212 , HIS C:213 , ALA C:220 , HIS C:233 , HEC C:1248 , TYR D:156 , ALA D:237 , ALA D:238 , LYS D:242 , PHE D:243 , HIS D:246 , PRO D:247 , HOH D:2052 , HOH D:2053BINDING SITE FOR RESIDUE HEC D1248
7AC7SOFTWARETYR C:156 , ALA C:237 , ALA C:238 , LYS C:242 , PHE C:243 , HIS C:246 , PRO C:247 , SER D:208 , CYS D:209 , CYS D:212 , HIS D:213 , TRP D:222 , HIS D:233 , HEC D:1250BINDING SITE FOR RESIDUE HEC D1249
8AC8SOFTWAREHIS C:148 , ILE C:149 , SER C:152 , LYS C:153 , TYR C:156 , PRO C:231 , ALA C:238 , HEC C:1248 , CYS D:209 , HIS D:213 , GLY D:225 , MET D:227 , ASP D:228 , CYS D:229 , CYS D:232 , HIS D:233 , HEC D:1249BINDING SITE FOR RESIDUE HEC D1250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H21)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ala A:62 -Pro A:63
2Leu A:121 -Pro A:122
3Ala B:62 -Pro B:63
4Leu B:121 -Pro B:122
5His B:246 -Pro B:247
6Ala C:62 -Pro C:63
7Leu C:121 -Pro C:122
8His C:246 -Pro C:247
9Ala D:62 -Pro D:63
10Leu D:121 -Pro D:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H21)

(-) Exons   (0, 0)

(no "Exon" information available for 1H21)

(-) 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:240
 aligned with CYCX_DESDA | P81040 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:240
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
           CYCX_DESDA    40 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 279
               SCOP domains d1h21a_ A: Dimeric di-heme split-soret cytochrome c                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h21 A   8 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 247
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain B from PDB  Type:PROTEIN  Length:240
 aligned with CYCX_DESDA | P81040 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:240
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
           CYCX_DESDA    40 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 279
               SCOP domains d1h21b_ B: Dimeric di-heme split-soret cytochrome c                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h21 B   8 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 247
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain C from PDB  Type:PROTEIN  Length:240
 aligned with CYCX_DESDA | P81040 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:240
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
           CYCX_DESDA    40 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 279
               SCOP domains d1h21c_ C: Dimeric di-heme split-soret cytochrome c                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhh...............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h21 C   8 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 247
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain D from PDB  Type:PROTEIN  Length:240
 aligned with CYCX_DESDA | P81040 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:240
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
           CYCX_DESDA    40 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 279
               SCOP domains d1h21d_ D: Dimeric di-heme split-soret cytochrome c                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h21 D   8 GRFDQVGGAFGWKPHKLDPKECAQVAYDGYWYKGFGCGFGAFYSIVGLMGEKYGAPYNQFPFAMLEANKGGISDWGTICGALYGAAATFSLFWGRKEVHPMVNELFRWYEVTKLPIFNPGDAAQGVKGDLPMSASDSVLCHISVSKWCYENKIEATSKQRSERCGRLTADAAFKAAEIINTKIDQGKDFKSTFPMQASVSSCGECHMTKGNDANWAKGIMDCTPCHSGTAATQNKFVNHP 247
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1H21)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H21)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CYCX_DESDA | P81040)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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: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.

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(-) Related Entries Specified in the PDB File

1ddc DIMERIC DI-HEME SPLIT-SORET CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774