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(-) Description

Title :  CYTOCHROME C DOMAIN OF CAA3 OXYGEN OXIDOREDUCTASE
 
Authors :  V. Srinivasan, C. Rajendran, F. L. Sousa, A. M. P. Melo, L. M. Saraiva, M. M. Pereira, M. Santana, M. Teixeira, H. Michel
Date :  06 Jul 04  (Deposition) - 19 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Cytochrome C Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Srinivasan, C. Rajendran, F. L. Sousa, A. M. P. Melo, L. M. Saraiva, M. M. Pereira, M. Santana, M. Teixeira, H. Michel
Structure At 1. 3A Resolution Of Rhodothermus Marinus Caa(3) Cytochrome C Domain
J. Mol. Biol. V. 345 1047 2005
PubMed-ID: 15644203  |  Reference-DOI: 10.1016/J.JMB.2004.10.069

(-) Compounds

Molecule 1 - CYTOCHROME OXIDASE SUBUNIT II
    Chains: A
    EC Number: 1.9.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET-12A
    Fragment: CYTOCHROME C DOMAIN, RESIDUES 218-316
    Organism Scientific: RHODOTHERMUS MARINUS
    Organism Taxid: 29549

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:17 , SER A:20 , TYR A:38 , ASP A:53 , GLU A:54 , PRO A:73 , HOH A:2130 , HOH A:2131BINDING SITE FOR RESIDUE ACT A1102
2AC2SOFTWAREALA A:17 , CYS A:18 , CYS A:21 , HIS A:22 , VAL A:30 , PRO A:32 , LEU A:37 , ARG A:42 , TYR A:56 , LEU A:57 , SER A:60 , LYS A:67 , VAL A:68 , VAL A:69 , PRO A:73 , MET A:76 , PRO A:77 , TYR A:80 , HOH A:2046 , HOH A:2124 , HOH A:2125 , HOH A:2126BINDING SITE FOR RESIDUE HEM A1100
3AC3SOFTWAREARG A:42 , VAL A:69 , GLN A:70 , TYR A:72 , GLU A:85 , HOH A:2044 , HOH A:2058 , HOH A:2127 , HOH A:2128 , HOH A:2129BINDING SITE FOR RESIDUE TRS A1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W2L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W2L)

(-) Exons   (0, 0)

(no "Exon" information available for 1W2L)

(-) 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    
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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:97
 aligned with Q9F3S9_RHOMR | Q9F3S9 from UniProtKB/TrEMBL  Length:316

    Alignment length:97
                                   229       239       249       259       269       279       289       299       309       
         Q9F3S9_RHOMR   220 MPLAELGARLYREKACFSCHSIDGSRLVGPSFKGLYGSTRTFEDGTTAVADENYLRESILQPGAKVVQGYPNVMPASYASLSEREVAALIEFIKQQQ 316
               SCOP domains d1w2la_ A: automated matches                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Cytochrome_CBB3-1w2lA01 A:4-95                                                              ---- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...................eee.....eee.hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1w2l A   3 MPLAELGARLYREKACFSCHSIDGSRLVGPSFKGLYGSTRTFEDGTTAVADENYLRESILQPGAKVVQGYPNVMPASYASLSEREVAALIEFIKQQQ  99
                                    12        22        32        42        52        62        72        82        92
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W2L)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9F3S9_RHOMR | Q9F3S9)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0004129    cytochrome-c oxidase activity    Catalysis of the reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O.
    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.
biological process
    GO:0022900    electron transport chain    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:1902600    hydrogen ion transmembrane transport    The directed movement of hydrogen ion (proton) across a membrane.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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