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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE RIESKE-TYPE FERREDOXIN ASSOCIATED WITH BIPHENYL DIOXYGENASE

Authors :   C. L. Colbert, M. M. -J. Couture, L. D. Eltis, J. T. Bolin

Date :   06 Sep 00 (Deposition) - 03 Jan 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A,B

Keywords :   Rieske-Type Ferredoxin, 2Fe-2S Cluster, Beta Sandwich, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Colbert, M. M. Couture, L. D. Eltis, J. T. Bolin
A Cluster Exposed: Structure Of The Rieske Ferredoxin From Biphenyl Dioxygenase And The Redox Properties Of Rieske Fe- Proteins.
Structure Fold. Des. V. 8 1267 2000
PubMed-ID: 11188691 | Reference-DOI: 10.1016/S0969-2126(00)00536-0

Molecule 1 - RIESKE-TYPE FERREDOXIN OF BIPHENYL DIOXYGENASE
	Chains	:	A, B
	EC Number	:	1.14.12.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEBRE12
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	BURKHOLDERIA XENOVORANS
	Organism Taxid	:	266265
	Strain	:	LB400
	Synonym	:	BIPHENYL DIOXYGENASE, BIPHENYL DIOXYGENASE SYSTEM FERREDOXIN COMPONENT, BIPHENYL DIOXYGENASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	GOL	3	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:43 , HIS A:45 , GLY A:46 , CYS A:63 , HIS A:66 , GLY A:68	BINDING SITE FOR RESIDUE FES A 1001
2	AC2	SOFTWARE	CYS B:43 , HIS B:45 , GLY B:46 , CYS B:63 , HIS B:66 , GLY B:68	BINDING SITE FOR RESIDUE FES B 2002
3	AC3	SOFTWARE	GLU A:84 , ALA A:85 , HOH A:322 , HOH A:325 , ARG B:5 , VAL B:6 , GLU B:21 , HOH B:318 , HOH B:324	BINDING SITE FOR RESIDUE GOL A 901
4	AC4	SOFTWARE	GLU A:35 , LEU A:36 , HIS A:45 , PRO A:81 , ILE A:91 , ILE A:93 , HOH A:327 , HOH A:546	BINDING SITE FOR RESIDUE GOL A 902
5	AC5	SOFTWARE	GLU B:35 , LEU B:36 , HIS B:45 , ILE B:91 , ILE B:93 , HOH B:326 , HOH B:490	BINDING SITE FOR RESIDUE GOL B 903

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:80	-	Pro A:81
2	Pro B:80	-	Pro B:81

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIESKE	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.	BPHF_PARXL	4-100	2	A:4-100 B:4-100

(no "Exon" information available for 1FQT)

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 A from PDB  Type:PROTEIN  Length:109
 aligned with BPHF_PARXL | P37332 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:109
                                    10        20        30        40        50        60        70        80        90       100         
           BPHF_PARXL     1 MKFTRVCDRRDVPEGEALKVESGGTSVAIFNVDGELFATQDRCTHGDWSLSDGGYLEGDVVECSLHMGKFCVRTGKVKSPPPCEALKIFPIRIEDNDVLVDFEAGYLAP 109
               SCOP domains d1fqta_ A: Rieske-type ferredoxin associated with biphenyl dioxygenase                                        SCOP domains
               CATH domains 1fqtA00 A:1-109 'Rieske'-like iron-sulphur domains                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhh....eeeeee..eeeeeeee..eeeeee...............ee..eee......eee.....eee...........eeee..eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RIESKE  PDB: A:4-100 UniProt: 4-100                                                              --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1fqt A   1 MKFTRVCDRRDVPEGEALKVESGGTSVAIFNVDGELFATQDRCTHGDWSLSDGGYLEGDVVECSLHMGKFCVRTGKVKSPPPCEALKIFPIRIEDNDVLVDFEAGYLAP 109
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with BPHF_PARXL | P37332 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:109
                                    10        20        30        40        50        60        70        80        90       100         
           BPHF_PARXL     1 MKFTRVCDRRDVPEGEALKVESGGTSVAIFNVDGELFATQDRCTHGDWSLSDGGYLEGDVVECSLHMGKFCVRTGKVKSPPPCEALKIFPIRIEDNDVLVDFEAGYLAP 109
               SCOP domains d1fqtb_ B: Rieske-type ferredoxin associated with biphenyl dioxygenase                                        SCOP domains
               CATH domains 1fqtB00 B:1-109 'Rieske'-like iron-sulphur domains                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhh....eeeeee..eeeeeeee..eeeeee.............eeee..eeee.....eee.....eee........ee.eeee..eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RIESKE  PDB: B:4-100 UniProt: 4-100                                                              --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1fqt B   1 MKFTRVCDRRDVPEGEALKVESGGTSVAIFNVDGELFATQDRCTHGDWSLSDGGYLEGDVVECSLHMGKFCVRTGKVKSPPPCEALKIFPIRIEDNDVLVDFEAGYLAP 109
                                    10        20        30        40        50        60        70        80        90       100

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: ISP domain (115)

Superfamily: ISP domain (115)

Family: Rieske iron-sulfur protein (ISP) (50)

Protein domain: Rieske-type ferredoxin associated with biphenyl dioxygenase (1)

Burkholderia cepacia [TaxId: 292] (1)

1a	d1fqta_	A:
1b	d1fqtb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: 3-layer Sandwich (102)

Topology: Rieske Iron-sulfur Protein (99)

Homologous Superfamily: 'Rieske'-like iron-sulphur domains (99)

Burkholderia xenovorans lb400. Organism_taxid: 266265. Strain: lb400. (1)

1a	1fqtA00	A:1-109
1b	1fqtB00	B:1-109

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BPHF_PARXL | P37332)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	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.

Asymmetric/Biological Unit
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1ndo	CONTAINS A RIESKE DOMAIN IN THE LARGE SUBUNIT
1rfs	RIESKE PROTEIN FROM SPINACH CHLOROPLAST
1rie	RIESKE PROTEIN FROM BOVINE MITOCHONDRIA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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