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Asym./Biol. Unit

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Description

Title :   X-RAY STRUCTURE OF THE M100K VARIANT OF FERRIC CYT C-550 FROM PARACOCCUS VERSUTUS DETERMINED AT 295 K.

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

Date :   07 Jan 05 (Deposition) - 11 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : X

Keywords :   C-Type Cytochrome, Heme, Electron Transfer, Axial Ligand, 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	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC19_M100K/PEC86
	Expression System Strain	:	MV1190
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	PARACOCCUS VERSUTUS
	Organism Taxid	:	34007

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	LYS X:14 , CYS X:15 , CYS X:18 , HIS X:19 , THR X:35 , ARG X:45 , ALA X:48 , TYR X:55 , GLY X:56 , ILE X:59 , TRP X:71 , LEU X:76 , TYR X:79 , PRO X:85 , LYS X:99 , LYS X:100 , HOH X:2014 , HOH X:2031 , HOH X:2032	BINDING SITE FOR RESIDUE HEC X1123

SS Bonds (0, 0)

(no "SS Bond" information available for 2BH5)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2BH5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2BH5)

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 2BH5)

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:122
 aligned with CY550_PARVE | Q00499 from UniProtKB/Swiss-Prot  Length:154

    Alignment length:122
                                    31        41        51        61        71        81        91       101       111       121       131       141  
          CY550_PARVE    22 EGDAAKGEKEFNKCKACHMVQAPDGTDIVKGGKTGPNLYGVVGRKIASVEGFKYGDGILEVAEKNPDMVWSEADLIEYVTDPKPWLVEKTGDSAAKTKMTFKLGKNQADVVAFLAQHSPDAG 143
               SCOP domains d2bh5x_ X: automated matches                                                                                               SCOP domains
               CATH domains 2bh5X00 X:2-123 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
                 2bh5 X   2 EGDAAKGEKEFNKCKACHMVQAPDGTDIVKGGKTGPNLYGVVGRKIASVEGFKYGDGILEVAEKNPDMVWSEADLIEYVTDPKPWLVEKTGDSAAKTKKTFKLGKNQADVVAFLAQHSPDAG 123
                                    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)

d2bh5x_

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)

2bh5X00

X:2-123

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2BH5)

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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Asymmetric/Biological Unit
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	Sites
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	Cis Peptide Bonds
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Still Images

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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

Related Entries Specified in the PDB File

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