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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C'' FROM METHYLOPHILUS METHYLOTROPHUS
 
Authors :  F. J. Enguita, E. Pohl, A. Rodrigues, H. Santos, M. A. Carrondo
Date :  22 Jan 02  (Deposition) - 16 Jan 03  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase(Cytochrome), Oxidoreductase, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. J. Enguita, E. Pohl, D. L. Turner, H. Santos, M. A. Carrondo
Structural Evidence For A Proton Transfer Pathway Coupled With Haem Reduction Of Cytochrome C" From Methylophilus Methylotrophus.
J. Biol. Inorg. Chem. V. 11 189 2006
PubMed-ID: 16341897  |  Reference-DOI: 10.1007/S00775-005-0065-6

(-) Compounds

Molecule 1 - CYTOCHROME C''
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: METHYLOPHILUS METHYLOTROPHUS
    Organism Taxid: 2327
    Strain: W3A1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HEC2Ligand/IonHEME C
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:34 , ALA A:48 , CYS A:49 , CYS A:52 , HIS A:53 , ASN A:63 , PRO A:71 , LEU A:73 , ARG A:81 , GLU A:91 , HIS A:95 , ILE A:99 , HOH A:2185 , HOH A:2186 , HOH A:2187 , HOH A:2188 , HOH A:2189 , HOH A:2190BINDING SITE FOR RESIDUE HEC A 125
2AC2SOFTWAREPHE B:34 , CYS B:49 , CYS B:52 , HIS B:53 , ASN B:63 , PRO B:71 , LEU B:73 , ARG B:81 , VAL B:88 , HIS B:95 , ILE B:99 , HOH B:2120 , HOH B:2164 , HOH B:2165 , HOH B:2166 , HOH B:2167BINDING SITE FOR RESIDUE HEC B 125

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:96 -A:104
2B:96 -B:104

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GU2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GU2)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYCA_METME46-140
 		  2A:26-120
B:26-120
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYCA_METME46-140
 		  1A:26-120
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYCA_METME46-140
 		  1-
B:26-120

(-) Exons   (0, 0)

(no "Exon" information available for 1GU2)

(-) 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:124
 aligned with CYCA_METME | Q9RQB9 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:124
                                    30        40        50        60        70        80        90       100       110       120       130       140    
           CYCA_METME    21 DVTNAEKLVYKYTNIAHSANPMYEAPSITDGKIFFNRKFKTPSGKEAACASCHTNNPANVGKNIVTGKEIPPLAPRVNTKRFTDIDKVEDEFTKHCNDILGADCSPSEKANFIAYLLTETKPTK 144
               SCOP domains d1gu2a_ A: Cytochrome c''                                                                                                    SCOP domains
               CATH domains 1gu2A00 A:1-124 Cytochrome c                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.ee.....eehhhhhhh......ee......ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------CYTC  PDB: A:26-120 UniProt: 46-140                                                            ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gu2 A   1 DVTNAEKLVYKYTNIAHSANPMYEAPSITDGKIFFNRKFKTPSGKEAACASCHTNNPANVGKNIVTGKEIPPLAPRVNTKRFTDIDKVEDEFTKHCNDILGADCSPSEKANFIAYLLTETKPTK 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with CYCA_METME | Q9RQB9 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:123
                                    30        40        50        60        70        80        90       100       110       120       130       140   
           CYCA_METME    21 DVTNAEKLVYKYTNIAHSANPMYEAPSITDGKIFFNRKFKTPSGKEAACASCHTNNPANVGKNIVTGKEIPPLAPRVNTKRFTDIDKVEDEFTKHCNDILGADCSPSEKANFIAYLLTETKPT 143
               SCOP domains d1gu2b_ B: Cytochrome c''                                                                                                   SCOP domains
               CATH domains 1gu2B00 B:1-123 Cytochrome c                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.ee.....eehhhhhhh......ee......ee.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------CYTC  PDB: B:26-120 UniProt: 46-140                                                            --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gu2 B   1 DVTNAEKLVYKYTNIAHSANPMYEAPSITDGKIFFNRKFKTPSGKEAACASCHTNNPANVGKNIVTGKEIPPLAPRVNTKRFTDIDKVEDEFTKHCNDILGADCSPSEKANFIAYLLTETKPT 123
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GU2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CYCA_METME | Q9RQB9)
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:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CYCA_METME | Q9RQB9: 1e8e 1oae

(-) Related Entries Specified in the PDB File

1e8e SOLUTION STRUCTURE OF METHYLOPHILUS METHYLOTROPHUS CYTOCHROME C'': INSIGHTS INTO THE STRUCTURAL BASIS OF HAEM-LIGAND DETACHMENT