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(-) Description

Title :  REDUCED SOXAX COMPLEX FROM RHODOVULUM SULFIDOPHILUM
 
Authors :  V. A. Bamford, S. Bruno, T. Rasmussen, C. Appia-Ayme, M. R. Cheesman, B. C. Berks, A. M. Hemmings
Date :  21 Aug 02  (Deposition) - 07 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Electron Transfer, Sulfur Cycle, Soxax Complex, Thiosulfate Oxidation, Cysteine Persulfide Heme Ligand, Cytochrome C (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. A. Bamford, S. Bruno, T. Rasmussen, C. Appia-Ayme, M. R. Cheesman, B. C. Berks, A. M. Hemmings
Structural Basis For The Oxidation Of Thiosulfate By A Sulfur Cycle Enzyme
Embo J. V. 21 5599 2002
PubMed-ID: 12411478  |  Reference-DOI: 10.1093/EMBOJ/CDF566

(-) Compounds

Molecule 1 - DIHEME CYTOCHROME C
    Chains: A
    Organism Scientific: RHODOVULUM SULFIDOPHILUM
    Organism Taxid: 35806
    Synonym: SOXA
 
Molecule 2 - CYTOCHROME C
    Chains: B
    Organism Scientific: RHODOVULUM SULFIDOPHILUM
    Organism Taxid: 35806
    Synonym: SOXX

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3HEC3Ligand/IonHEME C

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:192 , ARG A:206 , ARG A:218 , HEC A:1264 , HOH A:2445BINDING SITE FOR RESIDUE EDO A1262
2AC2SOFTWAREALA A:75 , CYS A:76 , CYS A:79 , HIS A:80 , LEU A:90 , TYR A:94 , CYS A:114 , ARG A:118 , MET A:119 , HOH A:2204 , HOH A:2209 , HOH A:2237 , HOH A:2262 , HOH A:2448 , HOH A:2451 , HOH A:2453 , HOH A:2454 , PHE B:56 , HOH B:2052BINDING SITE FOR RESIDUE HEC A1263
3AC3SOFTWAREGLY A:34 , ARG A:38 , SER A:176 , CYS A:177 , CYS A:180 , HIS A:181 , ILE A:189 , HIS A:193 , LEU A:194 , SER A:195 , GLY A:197 , GLN A:198 , ILE A:199 , PHE A:202 , ARG A:218 , PHE A:219 , CSS A:222 , ILE A:223 , ARG A:260 , EDO A:1262 , HOH A:2455 , HOH A:2456 , HOH A:2457 , HOH A:2458 , EDO B:1138BINDING SITE FOR RESIDUE HEC A1264
4AC4SOFTWAREHEC A:1264 , HOH A:2420 , ASN B:41 , ALA B:44 , HOH B:2204 , HOH B:2205 , HOH B:2206BINDING SITE FOR RESIDUE EDO B1138
5AC5SOFTWAREHOH A:2357 , GLY B:40 , CYS B:42 , CYS B:45 , HIS B:46 , VAL B:60 , PRO B:62 , LEU B:64 , ARG B:70 , TYR B:71 , ILE B:79 , LEU B:80 , PHE B:87 , THR B:90 , VAL B:91 , MET B:92 , TYR B:95 , MET B:121 , VAL B:129 , HOH B:2122 , HOH B:2207 , HOH B:2208BINDING SITE FOR RESIDUE HEC B1139

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H32)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:94 -Pro A:95
2Phe A:202 -Pro A:203
3Gly A:256 -Pro A:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H32)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.SOXA_RHOSU74-168  1A:48-142

(-) Exons   (0, 0)

(no "Exon" information available for 1H32)

(-) 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:261
 aligned with SOXA_RHOSU | Q939U1 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:261
                                    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 
           SOXA_RHOSU    27 GPDDPLVINGEIEIVTRAPTPAHLADRFDEIRSGWTFRTDDTQALEMDDFENSGMVFVEEARAVWDRPEGTEGKACADCHGAVDDGMYGLRAVYPKYVESAGKVRTVEQMINACRTSRMGAPEWDYIGPDMTAMVALIASVSRGMPVSVAIDGPAQSTWEKGREIYYTRYGQLDLSCASCHEQYFDHYIRADHLSQGQINGFPSYRLKNARLNAVHDRFRGCIRDTRGVPFAVGSPEFVALELYVASRGNGLSVEGPSVRN 287
               SCOP domains d1h32a1 A:1-150 Di-heme cytochrome c SoxA                                                                                                             d1h32a2 A:151-261 Di-heme cytochrome c SoxA                                                                     SCOP domains
               CATH domains 1h32A01 A:1-54,A:146-260 Cytochrome c                 1h32A02 A:55-142 Cytochrome c                                                           ---1h32A01 A:1-54,A:146-260 Cytochrome c                                                                              - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...eee..ee..hhhhh.....ee.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.hhhhhh.ee......eehhhhhhhhhhhhh.........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh........hhhhhhh.....ee..ee..........eee....eeehhhhhhhhhhhh.........hhhhhhhhhhhhhhh........eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------CYTC  PDB: A:48-142 UniProt: 74-168                                                            ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h32 A   1 GPDDPLVINGEIEIVTRAPTPAHLADRFDEIRSGWTFRTDDTQALEMDDFENSGMVFVEEARAVWDRPEGTEGKACADCHGAVDDGMYGLRAVYPKYVESAGKVRTVEQMINACRTSRMGAPEWDYIGPDMTAMVALIASVSRGMPVSVAIDGPAQSTWEKGREIYYTRYGQLDLSCASCHEQYFDHYIRADHLSQGQINGFPSYRLKNARLNAVHDRFRGcIRDTRGVPFAVGSPEFVALELYVASRGNGLSVEGPSVRN 261
                                    10        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 
                                                                                                                                                                                                                                                       222-CSS                                   


Chain B from PDB  Type:PROTEIN  Length:135
 aligned with Q939U4_RHOSU | Q939U4 from UniProtKB/TrEMBL  Length:160

    Alignment length:138
                                    32        42        52        62        72        82        92       102       112       122       132       142       152        
         Q939U4_RHOSU    23 AEVAPGDVAIDGQGHVARPLTDAPGDPVEGRRLMTDRSVGNCIACHEVTEMADAQFPGTVGPSLDGVAARYPEAMIRGILVNSKNVFPETVMPAYYRVEGFNRPGIAFTSKPIEGEIRPLMTAGQIEDVVAYLMTLTQ 160
               SCOP domains d1h32b_ B: Mono-heme c-type cytochrome SoxX                                                                                                SCOP domains
               CATH domains 1h32B00 B:1-138 Cytochrome c                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.................hhhhhhhhhhh....hhhhh......---...........hhhhhhhhhhhhhhhhhhhhhh..................................hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h32 B   1 AEVAPGDVAIDGQGHVARPLTDAPGDPVEGRRLMTDRSVGNCIACHEVTEM---QFPGTVGPSLDGVAARYPEAMIRGILVNSKNVFPETVMPAYYRVEGFNRPGIAFTSKPIEGEIRPLMTAGQIEDVVAYLMTLTQ 138
                                    10        20        30        40        50|   |   60        70        80        90       100       110       120       130        
                                                                             51  55
   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, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H32)

(-) Gene Ontology  (14, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SOXA_RHOSU | Q939U1)
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.
    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.
    GO:0016669    oxidoreductase activity, acting on a sulfur group of donors, cytochrome as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces a cytochrome.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0016783    sulfurtransferase activity    Catalysis of the transfer of sulfur atoms from one compound (donor) to another (acceptor).
biological process
    GO:0018192    enzyme active site formation via cysteine modification to L-cysteine persulfide    The formation of an enzyme active site via modification of peptidyl-cysteine to peptidyl-L-cysteine persulfide.
    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.
    GO:0019418    sulfide oxidation    The chemical reactions and pathways resulting in the conversion of sulfide to elemental sulfur in a higher oxidation state, or to sulfite or sulfate.
    GO:0019417    sulfur oxidation    The chemical reactions and pathways resulting the addition of oxygen to elemental sulfur.
cellular component
    GO:0070069    cytochrome complex    A protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
    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 B   (Q939U4_RHOSU | Q939U4)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).

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  SOXA_RHOSU | Q939U1
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 Related Entries

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

UniProtKB/Swiss-Prot
        SOXA_RHOSU | Q939U1: 1h31 1h33 2oz1
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        Q939U4_RHOSU | Q939U4: 1h31 1h33 2oz1

(-) Related Entries Specified in the PDB File

1h31 OXIDISED SOXAX COMPLEX FROM RHODOVULUM SULFIDOPHILUM
1h33 OXIDISED SOXAX COMPLEX FROM RHODOVULUM SULFIDOPHILUM