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Description

Title :   X-RAY STRUCTURE OF FERRIC CYTOCHROME C-550 FROM PARACOCCUS VERSUTUS

Authors :   J. A. R. Worrall, A. -M. M. Van Roon, M. Ubbink, G. W. Canters

Date :   05 Jan 05 (Deposition) - 11 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : X

Keywords :   C-Type Cytochrome, Heme Group, Electron Transfer, Pyrrolidone Carboxylic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. R. Worrall, A. -M. M. Van Roon, M. Ubbink, G. W. Canters
The Effect Of Replacing The Axial Methionine Ligand With A Lysine Residue In Cytochrome C-550 From Paracoccus Versutus Assessed By X-Ray Crystallography And Unfolding.
Febs J. V. 272 2441 2005
PubMed-ID: 15885094 | Reference-DOI: 10.1111/J.1742-4658.2005.04664.X

Compounds

Molecule 1 - CYTOCHROME C-550
	Chains	:	X
	Engineered	:	YES
	Expression System	:	PARACOCCUS DENITRIFICANS
	Expression System Plasmid	:	PEG400.TV1
	Expression System Strain	:	2131
	Expression System Taxid	:	266
	Organism Scientific	:	PARACOCCUS VERSUTUS
	Organism Taxid	:	34007
	Other Details	:	HEME, PROTOPORPHYRIN IX

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	X

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 1)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C

Sites (1, 1)

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS X:15 , CYS X:18 , HIS X:19 , THR X:35 , ARG X:45 , ALA X:48 , TYR X:55 , GLY X:56 , TRP X:71 , LEU X:76 , TYR X:79 , VAL X:80 , LYS X:99 , MET X:100 , HOH X:2018 , HOH X:2033 , HOH X:2042	BINDING SITE FOR RESIDUE HEC X1121

SS Bonds (0, 0)

(no "SS Bond" information available for 2BGV)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2BGV)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2BGV)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTC	PS51007	Cytochrome c family profile.	CY550_PARVE	23-139	1	X:3-119

Exons (0, 0)

(no "Exon" information available for 2BGV)

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:120
 aligned with CY550_PARVE | Q00499 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:120
                                    31        41        51        61        71        81        91       101       111       121       131       141
          CY550_PARVE    22 EGDAAKGEKEFNKCKACHMVQAPDGTDIVKGGKTGPNLYGVVGRKIASVEGFKYGDGILEVAEKNPDMVWSEADLIEYVTDPKPWLVEKTGDSAAKTKMTFKLGKNQADVVAFLAQHSPD 141
               SCOP domains d2bgvx_ X: automated matches                                                                                             SCOP domains
               CATH domains 2bgvX00 X:2-121 Cytochrome c                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....ee.....eee.........................hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -CYTC  PDB: X:3-119 UniProt: 23-139                                                                                   -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bgv X   2 EGDAAKGEKEFNKCKACHMVQAPDGTDIVKGGKTGPNLYGVVGRKIASVEGFKYGDGILEVAEKNPDMVWSEADLIEYVTDPKPWLVEKTGDSAAKTKMTFKLGKNQADVVAFLAQHSPD 121
                                    11        21        31        41        51        61        71        81        91       101       111       121

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, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome c (308)

Superfamily: Cytochrome c (308)

Family: monodomain cytochrome c (197)

Protein domain: automated matches (20)

Paracoccus versutus [TaxId: 34007] (3)

d2bgvx_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome Bc1 Complex; Chain D, domain 2 (279)

Homologous Superfamily: Cytochrome c (279)

Paracoccus versutus. Organism_taxid: 34007. (3)

2bgvX00

X:2-121

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2BGV)

Gene Ontology (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (CY550_PARVE | Q00499)

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.

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	Sites
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	Cis Peptide Bonds
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Still Images

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	2bgv
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CY550_PARVE \| Q00499	:	2bh4 2bh5

Related Entries Specified in the PDB File

2bh4	X-RAY STRUCTURE OF THE M100K VARIANT OF FERRIC CYT C-550 FROM PARACOCCUS VERSUTUS DETERMINED AT 100 K.
2bh5	X-RAY STRUCTURE OF THE M100K VARIANT OF FERRIC CYT C-550 FROM PARACOCCUS VERSUTUS DETERMINED AT 295 K.