1E85 - JenaLib

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Description

Title :   CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS-REDUCED STRUCTURE WITH NO BOUND TO PROXIMAL SIDE OF HEME

Authors :   D. M. Lawson, C. E. M. Stevenson, C. R. Andrew, R. R. Eady

Date :   15 Sep 00 (Deposition) - 06 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Electron Transport, Cytochrome, Heme, 4-Helix Bundle, Nitric Oxide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Lawson, C. E. M. Stevenson, C. R. Andrew, R. R. Eady
Unprecedented Proximal Binding Of Nitric Oxide To Heme: Implications For Guanylate Cyclase.
Embo J. V. 19 5661 2000
PubMed-ID: 11060017 | Reference-DOI: 10.1093/EMBOJ/19.21.5661
(for further references see the PDB file header)

Compounds

Molecule 1 - CYTOCHROME C'
	Cellular Location	:	PERIPLASM
	Chains	:	A
	Organism Scientific	:	ACHROMOBACTER XYLOSOXIDANS
	Organism Taxid	:	85698
	Other Details	:	FORMERLY KNOWN AS ALCALIGENES SP.
	Strain	:	NCIB 11015

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	HEC	1	Ligand/Ion	HEME C
2	NO	1	Ligand/Ion	NITIRC OXIDE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	HEC	2	Ligand/Ion	HEME C
2	NO	-1	Ligand/Ion	NITIRC OXIDE
3	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:12 , GLN A:13 , LEU A:16 , THR A:17 , MET A:19 , ALA A:20 , TRP A:56 , GLY A:66 , ASP A:67 , ILE A:72 , GLN A:83 , PHE A:86 , CYS A:116 , CYS A:119 , TYR A:123 , ARG A:124 , NO A:130 , HOH A:2202 , HOH A:2203 , HOH A:2204	BINDING SITE FOR RESIDUE HEC A 128
2	AC2	SOFTWARE	HIS A:120 , ARG A:124 , HEC A:128	BINDING SITE FOR RESIDUE NO A 130

SS Bonds (0, 0)

(no "SS Bond" information available for 1E85)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1E85)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1E85)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTCII	PS51009	Cytochrome c class II profile.	CYCP_ALCXX	7-125	1	A:7-125

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTCII	PS51009	Cytochrome c class II profile.	CYCP_ALCXX	7-125	2	A:7-125

Exons (0, 0)

(no "Exon" information available for 1E85)

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
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Chain A from PDB  Type:PROTEIN  Length:125
 aligned with CYCP_ALCXX | P00138 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
           CYCP_ALCXX     1 QFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRK 125
               SCOP domains d1e85a_ A: Cytochrome c'                                                                                                      SCOP domains
               CATH domains -1e85A00 A:2-125  [code=1.20.120.10, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CYTCII  PDB: A:7-125 UniProt: 7-125                                                                                     PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e85 A   1 xFAKPEDAVKYRQSALTLMASHFGRMTPVVKGQAPYDAAQIKANVEVLKTLSALPWAAFGPGTEGGDARPEIWSDAASFKQKQQAFQDNIVKLSAAADAGDLDKLRAAFGDVGASCKACHDAYRK 125
                            |       10        20        30        40        50        60        70        80        90       100       110       120     
                            |                                                                                                                            
                            1-PCA

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: Cytochromes (82)

Family: Cytochrome c'-like (44)

Protein domain: Cytochrome c' (16)

Alcaligenes sp. [TaxId: 512] (5)

d1e85a_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.10, no name defined] (45)

Achromobacter xylosoxidans. Organism_taxid: 85698. Strain: ncib 11015. (1)

1e85A00

A:2-125

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1E85)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A (CYCP_ALCXX | P00138)

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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0022900	electron transport chain	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: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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	CYCP_ALCXX \| P00138	:	1cgn 1cgo 1e83 1e84 1e86 2xl6 2xl8 2xld 2xle 2xlh 2xlm 2xlo 2xlv 2xlw 2xm0 2xm4 2ykz 2yl0 2yl1 2yl3 2yl7 2yld 2ylg 2yli 3zqv 3zqy 3ztm 3ztz 3zwi 4cda 4cdv 4cdy 4cip 4cjg 4cjo 4d4n 4d4x 4wgy 4wgz 5agf 5jli 5jp7 5jra 5js5 5jsl 5jt4 5jua 5jve

Related Entries Specified in the PDB File

1cgo	CYTOCHROME C'
1e83	CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - OXIDIZED STRUCTURE
1e84	CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE
1e86	CYTOCHROME C' FROM ALCALIGENES XYLOSOXIDANS - REDUCED STRUCTURE WITH CO BOUND TO DISTAL SIDE OF HEME