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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REDUCED FORM OF CYTOCHROME C" FROM METHYLOPHILUS METHYLOTROPHUS
 
Authors :  F. J. Enguita, R. Grenha, H. Santos, M. A. Carrondo
Date :  09 Jan 03  (Deposition) - 26 Mar 04  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase(Cytochrome), Cytochrome C, 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"
    ChainsA, B
    Organism ScientificMETHYLOPHILUS METHYLOTROPHUS
    Organism Taxid17

 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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2HEC1Ligand/IonHEME C
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HEC1Ligand/IonHEME C
3SO43Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:7 , HOH A:2118 , HOH A:2120 , HOH A:2121 , ALA B:102 , ASP B:103BINDING SITE FOR RESIDUE SO4 A1129
02AC2SOFTWARELYS A:80 , ARG A:81 , PHE A:82 , VAL A:88 , GLU A:91 , HEC A:1125 , HOH A:2122 , HOH A:2123 , HOH A:2124BINDING SITE FOR RESIDUE SO4 A1130
03AC3SOFTWAREASN A:59 , VAL A:60 , HOH A:2125 , HOH A:2126 , HOH A:2127BINDING SITE FOR RESIDUE SO4 A1131
04AC4SOFTWAREASN A:97 , ALA A:102 , ASP A:103 , LYS B:7 , LYS B:45 , HOH B:2096 , HOH B:2137 , HOH B:2138 , HOH B:2139BINDING SITE FOR RESIDUE SO4 B1128
05AC5SOFTWAREARG B:81 , PHE B:82 , LYS B:87 , VAL B:88 , GLU B:91 , HEC B:1125 , HOH B:2140BINDING SITE FOR RESIDUE SO4 B1129
06AC6SOFTWARESER B:27 , ILE B:28 , THR B:29 , HOH B:2142 , HOH B:2143BINDING SITE FOR RESIDUE SO4 B1130
07AC7SOFTWAREALA A:48 , CYS A:49 , CYS A:52 , HIS A:53 , ASN A:63 , ILE A:70 , PRO A:71 , LEU A:73 , ARG A:81 , GLU A:91 , PHE A:92 , HIS A:95 , ILE A:99 , SO4 A:1130 , HOH A:2112 , HOH A:2113BINDING SITE FOR RESIDUE HEC A1125
08AC8SOFTWAREPHE B:34 , CYS B:49 , CYS B:52 , HIS B:53 , ASN B:63 , ILE B:70 , PRO B:71 , LEU B:73 , ARG B:81 , GLU B:91 , PHE B:92 , HIS B:95 , ILE B:99 , SO4 B:1129 , HOH B:2132 , HOH B:2133 , HOH B:2134BINDING SITE FOR RESIDUE HEC B1125
09AC9SOFTWAREPRO A:26 , SER A:27 , ILE A:28 , THR A:29 , HOH A:2114 , HOH A:2115 , PRO B:21BINDING SITE FOR RESIDUE GOL A1126
10BC1SOFTWAREARG A:37 , GLU A:108 , HOH A:2101 , HOH A:2117 , PRO B:42BINDING SITE FOR RESIDUE GOL A1127
11BC2SOFTWAREILE A:33 , ARG A:37 , HOH A:2044 , HOH A:2050BINDING SITE FOR RESIDUE GOL A1128
12BC3SOFTWAREASN A:97 , HOH A:2090 , ILE B:64 , VAL B:65 , ILE B:99 , HOH B:2108 , HOH B:2135BINDING SITE FOR RESIDUE GOL B1126
13BC4SOFTWAREVAL A:65 , ILE A:99 , ASN B:97 , ASP B:98 , GLY B:101 , HOH B:2104 , HOH B:2112 , HOH B:2136BINDING SITE FOR RESIDUE GOL B1127

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1OAE)

(-) 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 d1oaea_ A: Cytochrome c''                                                                                                    SCOP domains
               CATH domains 1oaeA00 A:1-124 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: A:26-120 UniProt: 46-140                                                            ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oae A   1 DVTNAEKLVYKYTNIAHSANPMYEAPSITDGKIFFNRKFKTPSGKEAACASCHTNNPANVGKNIVTGKEIPPLAPRVNTKRFTDIDKVEDEFTKHCNDILGADCSPSEKANFIAYLLTETKPTK 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

Chain B 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 d1oaeb_ B: Cytochrome c''                                                                                                    SCOP domains
               CATH domains 1oaeB00 B:1-124 Cytochrome c                                                                                                 CATH domains
           Pfam domains (1) -----------------DUF1924-1oaeB01 B:18-116                                                                           -------- Pfam domains (1)
           Pfam domains (2) -----------------DUF1924-1oaeB02 B:18-116                                                                           -------- Pfam domains (2)
         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
                 1oae B   1 DVTNAEKLVYKYTNIAHSANPMYEAPSITDGKIFFNRKFKTPSGKEAACASCHTNNPANVGKNIVTGKEIPPLAPRVNTKRFTDIDKVEDEFTKHCNDILGADCSPSEKANFIAYLLTETKPTK 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

   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 Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) 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 | Q9RQB91e8e 1gu2

(-) Related Entries Specified in the PDB File

1e8e SOLUTION STRUCTURE OF METHYLOPHILUS METHYLOTROPHUS CYTOCHROME C'': INSIGHTS INTO THE STRUCTURAL BASIS OF HAEM-LIGAND DETACHMENT
1gu2 CRYSTAL STRUCTURE OF OXIDIZED CYTOCHROME C" FROM METHYLOPHILUS METHYLOTROPHUS