2EI3 - JenaLib

Title :   ANAEROBIC CRYSTAL STRUCTURE ANALYSIS OF THE 1,2-DIHYDROXYNAPHTHALENE DIOXYGENASE FROM PSEUDOMONAS SP. STRAIN C18 COMPLEXES WITH 2,3-DIHYDROXYBIPHENYL

Authors :   D. B. Neau, M. S. Kelker, C. L. Colbert, J. T. Bolin

Date :   10 Mar 07 (Deposition) - 19 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (8x)

Keywords :   Extradiol Dioxygenase, Protein Substrate Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. B. Neau, M. S. Kelker, H. Maaroufi, C. L. Colbert, L. D. Eltis, J. T. Bolin
Structural Explanation For Success And Failure In The Enzymatic Ring-Cleavage Of 3, 4 Dihydroxybiphenyl And Relate Pcb Metabolites
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:177 , HOH A:906 , HOH A:907 , HOH A:908 , HOH A:909 , HOH A:910	BINDING SITE FOR RESIDUE MG A 398
2	AC2	SOFTWARE	HIS A:152 , HIS A:215 , TYR A:256 , GLU A:266 , BPY A:350 , HOH A:903 , HOH A:904	BINDING SITE FOR RESIDUE FE2 A 399
3	AC3	SOFTWARE	HIS A:152 , ILE A:154 , TYR A:178 , LEU A:190 , PHE A:192 , HIS A:200 , HIS A:215 , HIS A:247 , ASN A:249 , ASP A:250 , TYR A:256 , LEU A:297 , FE2 A:399	BINDING SITE FOR RESIDUE BPY A 350
4	AC4	SOFTWARE	GLY A:171 , ARG A:173 , HIS A:194 , CYS A:195 , ASN A:196 , ALA A:197 , ASP A:276	BINDING SITE FOR RESIDUE BPY A 351
5	AC5	SOFTWARE	ALA A:22 , PHE A:26 , ILE A:238 , THR A:259 , PRO A:260	BINDING SITE FOR RESIDUE BPY A 352
6	AC6	SOFTWARE	TYR A:12 , TRP A:51 , HIS A:52 , HIS A:53 , ARG A:103 , MET A:104 , PRO A:125 , ARG A:126	BINDING SITE FOR RESIDUE GOL A 901
7	AC7	SOFTWARE	TYR A:178 , LEU A:190 , PHE A:192 , HIS A:247 , TYR A:256 , HOH A:905	BINDING SITE FOR RESIDUE GOL A 902

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 3)

Exons (0, 0)

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
	(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:298
 aligned with NAHC_PSEU8 | P0A108 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:298
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
           NAHC_PSEU8     5 AAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIPLPNGMTAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGYGLDVKLS 302
               SCOP domains d2ei3a1 A:5-137 automated matches                                                                                                    d2ei3a2 A:138-302 automated matches                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee..hhhhhhhhhhhh...eee......eeeee.......eeee.....eeeeeeeee.hhhhhhhhhhhhhhh....ee.hhhhhhhhheeeeeeee.....eeeeeeee...................hhhhh..eeee...hhhhhhhhhhhh.....eeeeee.....eeeeeee........eee........eeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee................ee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----VOC  PDB: A:9-124 UniProt: 9-124                                                                                    ------------------------VOC  PDB: A:149-270 UniProt: 149-270                                                                                      -------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EXTRADIOL_DIOXYGENAS  ------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ei3 A   5 AAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIPLPNGMTAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGYGLDVKLS 302
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294

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, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (NAHC_PSEU8 | P0A108)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	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.
	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
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:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	GO:1901170	naphthalene catabolic process	The chemical reactions and pathways resulting in the breakdown of naphthalene.
	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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