2QPZ - JenaLib

Title :   NAPHTHALENE 1,2-DIOXYGENASE RIESKE FERREDOXIN

Authors :   E. N. Brown, S. Ramaswamy, A. Karlsson, R. Friemann, J. V. Parales, R. Parales, D. T. Gibson

Date :   25 Jul 07 (Deposition) - 02 Sep 08 (Release) - 09 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   Rieske Ferredoxin, 2Fe-2S, Aromatic Hydrocarbons Catabolism, Electron Transport, Iron, Iron-Sulfur, Metal-Binding, Plasmid, Transport, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. N. Brown, R. Friemann, A. Karlsson, J. V. Parales, M. M. Couture, L. D. Eltis, S. Ramaswamy
Determining Rieske Cluster Reduction Potentials.
J. Biol. Inorg. Chem. V. 13 1301 2008
PubMed-ID: 18719951 | Reference-DOI: 10.1007/S00775-008-0413-4
(for further references see the PDB file header)

Compounds

Molecule 1 - NAPHTHALENE 1,2-DIOXYGENASE SYSTEM FERREDOXIN SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDTG141
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NDOA, NAHAB, NDOC1
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Strain	:	NCIB 9816

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

Asymmetric/Biological Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_NDOA_PSEPU_001 *	V	3	E	NDOA_PSEPU	---	---	A	V	2	E
2	UniProt	VAR_NDOA_PSEPU_002 *	L	15	P	NDOA_PSEPU	---	---	A	L	14	P
3	UniProt	VAR_NDOA_PSEPU_003 *	S	49	A	NDOA_PSEPU	---	---	A	S	48	A
4	UniProt	VAR_NDOA_PSEPU_004 *	K	77	R	NDOA_PSEPU	---	---	A	K	76	R
5	UniProt	VAR_NDOA_PSEPU_005 *	Q	85	E	NDOA_PSEPU	---	---	A	Q	84	E
6	UniProt	VAR_NDOA_PSEPU_006 *	P	91	A	NDOA_PSEPU	---	---	A	P	90	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:103
 aligned with NDOA_PSEPU | P0A185 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:103
                                    11        21        31        41        51        61        71        81        91       101   
           NDOA_PSEPU     2 TVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYATDNLCTHGSARMSDGYLEGREIECPLHQGRFDVCTGKALCAPVTQNIKTYPVKIENLRVMIDLS 104
               SCOP domains d2qpza_ A: automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Rieske-2qpzA01 A:3-96                                                                         ------- Pfam domains
         Sec.struct. author ...eeeeee........eeeeee..eeeeeeee..eeeeee........hhhhheee..eee......eee.....eee........ee.eeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) -E-----------P---------------------------------A---------------------------R-------E-----A------------- SAPs(SNPs)
                    PROSITE ----RIESKE  PDB: A:5-100 UniProt: 6-101                                                             --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2qpz A   1 TVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYATDNLCTHGSARMSDGYLEGREIECPLHQGRFDVCTGKALCAPVTQNIKTYPVKIENLRVMIDLS 103
                                    10        20        30        40        50        60        70        80        90       100

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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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NDOA_PSEPU | P0A185)

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.

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