2EI2 - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE 1,2-DIHYDROXYNAPHTHALENE DIOXYGENASE FROM PSEUDOMONAS SP. STAIN C18

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 :   1.69

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

Keywords :   Extradiol Dioxygenase, 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

Molecule 1 - 1,2-DIHYDROXYNAPHTHALENE DIOXYGENASE
	Chains	:	A
	EC Number	:	1.13.11.-
	Engineered	:	YES
	Expression System	:	PSEUDOMONAS PUTIDA
	Expression System Plasmid	:	PHMPVDG
	Expression System Strain	:	KT2442
	Expression System Taxid	:	303
	Expression System Vector Type	:	PLASMID
	Gene	:	DOXG
	Organism Scientific	:	PSEUDOMONAS SP.
	Organism Taxid	:	69011
	Strain	:	C18

		1
Asymmetric Unit	:	A
Biological Unit 1 (8x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	FE2	1	Ligand/Ion	FE (II) ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 24)

No.	Name	Count	Type	Full Name
1	FE2	8	Ligand/Ion	FE (II) ION
2	GOL	16	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:177 , HOH A:905 , HOH A:906 , HOH A:907 , HOH A:908 , HOH A:932	BINDING SITE FOR RESIDUE MG A 398
2	AC2	SOFTWARE	HIS A:152 , HIS A:215 , TYR A:256 , GLU A:266 , HOH A:903 , HOH A:904	BINDING SITE FOR RESIDUE FE2 A 399
3	AC3	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
4	AC4	SOFTWARE	PHE A:192 , HIS A:247 , TYR A:256 , LEU A:297 , HOH A:904 , HOH A:1143	BINDING SITE FOR RESIDUE GOL A 902

(no "SS Bond" information available for 2EI2)

(no "Cis Peptide Bond" information available for 2EI2)

(no "SAP(SNP)/Variant" information available for 2EI2)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	NAHC_PSEU8	9-124 149-270	2	A:9-124 A:149-270
2	EXTRADIOL_DIOXYGENAS	PS00082	Extradiol ring-cleavage dioxygenases signature.	NAHC_PSEU8	245-266	1	A:245-266

Biological Unit 1 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	NAHC_PSEU8	9-124 149-270	16	A:9-124 A:149-270
2	EXTRADIOL_DIOXYGENAS	PS00082	Extradiol ring-cleavage dioxygenases signature.	NAHC_PSEU8	245-266	8	A:245-266

(no "Exon" information available for 2EI2)

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:299
 aligned with NAHC_PSEU8 | P0A108 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:299
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293         
           NAHC_PSEU8     4 QAAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIPLPNGMTAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGYGLDVKLS 302
               SCOP domains d2ei2a1 A:4-137 automated matches                                                                                                     d2ei2a2 A:138-302 automated matches                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhh...eee......eeeee.......eeee.....eeeeeeee..hhhhhhhhhhhhhhh....ee.hhhhhhhhheeeeeeee.....eeeeeeee...................hhhhh..eeee...hhhhhhhhhhhh..eeeeeeeee.....eeeeeeee.......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
                 2ei2 A   4 NAAVIELGYMGISVKDPDAWKSFATDMLGLQVLDEGEKDRFYLRMDYWHHRIVVHHNGQDDLEYLGWRVAGKPEFEALGQKLIDAGYKIRICDKVEAQERMVLGLMKTEDPGGNPTEIFWGPRIDMSNPFHPGRPLHGKFVTGDQGLGHCIVRQTDVAEAHKFYSLLGFRGDVEYRIPLPNGMTAELSFMHCNARDHSIAFGAMPAAKRLNHLMLEYTHMEDLGYTHQQFVKNEIDIALQLGIHANDKALTFYGATPSGWLIEPGWRGATAIDEAEYYVGDIFGHGVEATGYGLDVKLS 302
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Superfamily: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Family: automated matches (34)

Protein domain: automated matches (34)

Pseudomonas sp. [TaxId: 69011] (5)

1a	d2ei2a1	A:4-137
1b	d2ei2a2	A:138-302

(no "CATH Domain" information available for 2EI2)

(no "Pfam Domain" information available for 2EI2)

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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	1.13.11.-
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	NAHC_PSEU8 \| P0A108	:	2ehz 2ei0 2ei1 2ei3

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Ligands, Modified Residues, Ions (3, 4)

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