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(-) Description

Title :  PPCB, A CYTOCHROME C7 FROM GEOBACTER SULFURREDUCENS
 
Authors :  P. R. Pokkuluri, M. Schiffer
Date :  14 Jan 08  (Deposition) - 01 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Multiheme Cytochromes, Cytochrome C7 Geobacter Sulfurreducens, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Morgado, M. Bruix, V. Orshonsky, Y. Y. Londer, N. E. Duke, X. Yang, P. R. Pokkuluri, M. Schiffer, C. A. Salgueiro
Structural Insights Into The Modulation Of The Redox Properties Of Two Geobacter Sulfurreducens Homologous Triheme Cytochromes.
Biochim. Biophys. Acta V. 1777 1157 2008
PubMed-ID: 18534185  |  Reference-DOI: 10.1016/J.BBABIO.2008.04.043
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C3
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Gene: CYD-1
    Organism Scientific: GEOBACTER SULFURREDUCENS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1HEM6Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:42 , LYS A:43BINDING SITE FOR RESIDUE SO4 A 75
2AC2SOFTWAREMET A:4 , HIS A:17 , GLN A:21 , CYS A:27 , CYS A:30 , HIS A:31 , PRO A:35 , GLY A:36 , LYS A:37 , ILE A:38 , ASN B:12 , GLN B:21BINDING SITE FOR RESIDUE HEM A 72
3AC3SOFTWAREPHE A:15 , LYS A:19 , HIS A:20 , ILE A:23 , SER A:50 , CYS A:51 , CYS A:54 , HIS A:55 , LYS A:60 , PRO A:62 , LYS B:19BINDING SITE FOR RESIDUE HEM A 73
4AC4SOFTWAREPHE A:6 , THR A:7 , ALA A:8 , LYS A:9 , ASN A:10 , LYS A:43 , ALA A:46 , HIS A:47 , THR A:63 , LYS A:64 , CYS A:65 , CYS A:68 , HIS A:69BINDING SITE FOR RESIDUE HEM A 74
5AC5SOFTWAREASN A:12 , GLN A:21 , MET B:4 , PHE B:15 , HIS B:17 , GLN B:21 , CYS B:27 , CYS B:30 , HIS B:31 , PRO B:35 , GLY B:36 , LYS B:37 , ILE B:38BINDING SITE FOR RESIDUE HEM B 72
6AC6SOFTWARELYS A:60 , THR B:14 , PHE B:15 , LYS B:19 , HIS B:20 , SER B:50 , CYS B:51 , CYS B:54 , HIS B:55 , LYS B:60 , PRO B:62BINDING SITE FOR RESIDUE HEM B 73
7AC7SOFTWARETHR A:7 , GLY A:40 , MET A:45 , PHE B:6 , THR B:7 , ALA B:8 , LYS B:9 , ASN B:10 , GLY B:42 , LYS B:43 , ALA B:46 , HIS B:47 , LYS B:64 , CYS B:65 , CYS B:68 , HIS B:69BINDING SITE FOR RESIDUE HEM B 74

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BXU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BXU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BXU)

(-) 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:71
 aligned with Q74G83_GEOSL | Q74G83 from UniProtKB/TrEMBL  Length:91

    Alignment length:71
                                    30        40        50        60        70        80        90 
          Q74G83_GEOSL   21 ADTMTFTAKNGNVTFDHKKHQTIVPDCAVCHGKTPGKIEGFGKEMAHGKSCKGCHEEMKKGPTKCGECHKK 91
               SCOP domains d3bxua_ A: automated matches                                            SCOP domains
               CATH domains 3bxuA00 A:1-71 Cytochrome C3                                            CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....eeeehhhhhhhhh..hhhhhh.........hhhhhhh..hhhhhhhhh....hhhhhee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3bxu A  1 ADTMTFTAKNGNVTFDHKKHQTIVPDCAVCHGKTPGKIEGFGKEMAHGKSCKGCHEEMKKGPTKCGECHKK 71
                                    10        20        30        40        50        60        70 


Chain B from PDB  Type:PROTEIN  Length:71
 aligned with Q74G83_GEOSL | Q74G83 from UniProtKB/TrEMBL  Length:91

    Alignment length:71
                                    30        40        50        60        70        80        90 
          Q74G83_GEOSL   21 ADTMTFTAKNGNVTFDHKKHQTIVPDCAVCHGKTPGKIEGFGKEMAHGKSCKGCHEEMKKGPTKCGECHKK 91
               SCOP domains d3bxub_ B: automated matches                                            SCOP domains
               CATH domains 3bxuB00 B:1-71 Cytochrome C3                                            CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeeehhhhhhhh..hhhhhh.........hhhhhhh..hhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  3bxu B  1 ADTMTFTAKNGNVTFDHKKHQTIVPDCAVCHGKTPGKIEGFGKEMAHGKSCKGCHEEMKKGPTKCGECHKK 71
                                    10        20        30        40        50        60        70
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q74G83_GEOSL | Q74G83)
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:0006791    sulfur utilization    A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary sulfur sources and then activates genes to scavenge the last traces of the primary sulfur source and to transport and metabolize alternate sulfur sources. The utilization process begins when the cell or organism detects sulfur levels, includes the activation of genes whose products detect, transport or metabolize sulfur-containing compounds, and ends when the sulfur is incorporated into the cell or organism's metabolism.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1os6 CYTOCHROME C7 (PPCA) FROM GEOBACTER SULFURREDUCENS