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(-) Description

Title :  STRUCTURE OF THE SOLUBLE DOMAIN OF CYTOCHROME C552 WITH ITS FLEXIBLE LINKER SEGMENT FROM PARACOCCUS DENITRIFICANS
 
Authors :  C. Rajendran, U. Ermler, B. Ludwig, H. Michel
Date :  20 Mar 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.33
Chains :  Asym./Biol. Unit :  X
Keywords :  Electron Transport Chain (Cytochrome), Electron Transfer, P. Denitrificans, Electron Donor, Cell Membrane, Electron Transport, Heme, Iron, Membrane, Metal-Binding, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Rajendran, U. Ermler, B. Ludwig, H. Michel
Structure At 1. 5 A Resolution Of Cytochrome C(552) With Its Flexible Linker Segment, A Membrane-Anchored Protein From Paracoccus Denitrificans.
Acta Crystallogr. , Sect. D V. 66 850 2010
PubMed-ID: 20606266  |  Reference-DOI: 10.1107/S0907444910019396

(-) Compounds

Molecule 1 - CYTOCHROME C-552
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SOLUBLE DOMAIN WITH FLEXIBLE LINKER SEGMENT (UNP RESIDUES 38-176)
    Gene: CYCM
    Organism Scientific: PARACOCCUS DENITRIFICANS
    Organism Taxid: 266
    Synonym: CYTOCHROME C552

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1HEC1Ligand/IonHEME C
2ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS X:53 , CYS X:54 , CYS X:57 , HIS X:58 , VAL X:66 , PRO X:68 , ARG X:76 , ALA X:79 , PHE X:84 , TYR X:86 , SER X:87 , TRP X:97 , LEU X:102 , THR X:116 , LYS X:117 , MET X:118 , ALA X:119 , PHE X:120 , LEU X:132 , HOH X:255BINDING SITE FOR RESIDUE HEC X 141
2AC2SOFTWAREGLU X:9 , HIS X:69 , HOH X:199 , HOH X:246 , HOH X:334BINDING SITE FOR RESIDUE ZN X 142
3AC3SOFTWAREGLU X:8 , HIS X:10 , ASP X:82 , GLU X:127BINDING SITE FOR RESIDUE ZN X 143
4AC4SOFTWAREHIS X:3 , ASP X:88 , GLU X:100 , GLU X:104BINDING SITE FOR RESIDUE ZN X 144
5AC5SOFTWAREMET X:1 , GLU X:6 , HIS X:93 , HOH X:244BINDING SITE FOR RESIDUE ZN X 145

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M97)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M97)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M97)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CY552_PARDE78-176  1X:42-140

(-) Exons   (0, 0)

(no "Exon" information available for 3M97)

(-) 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 X from PDB  Type:PROTEIN  Length:118
 aligned with CY552_PARDE | P54820 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:140
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176
          CY552_PARDE    37 SGHGAEGEEHAQAYTYPVESAGGAEGEAVDEGPDFATVLASADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 176
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------Cytochrom_C-3m97X01 X:44-140                                                                      Pfam domains
         Sec.struct. author ...........----------------------hhhhhhhh.hhhhhhhhhhhh................................hhhhhhh....hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------CYTC  PDB: X:42-140 UniProt: 78-176                                                                 PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m97 X   1 MGHGAEGEEHA----------------------DFATVLASADPAAGEKVFGKCKACHKLDGNDGVGPHLNGVVGRTVAGVDGFNYSDPMKAHGGDWTPEALQEFLTNPKAVVKGTKMAFAGLPKIEDRANLIAYLEGQQ 140
                                    10|        -         -   |    40        50        60        70        80        90       100       110       120       130       140
                                     11                     34
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3M97)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M97)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (CY552_PARDE | P54820)
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: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.

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  3m97
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  CY552_PARDE | P54820
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 Related Entries

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

UniProtKB/Swiss-Prot
        CY552_PARDE | P54820: 1c7m 1i6d 1i6e 1ql3 1ql4 1zyy

(-) Related Entries Specified in the PDB File

1ql4 STRUCTURE OF THE SOLUBLE DOMAIN OF CYTOCHROME C(552) FROM PARACOCCUS DENITRIFICANS IN THE OXIDIZED AND REDUCED STATES