2Y99 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2,3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B-356 COMPLEX WITH CO-ENZYME NAD

Authors :   S. Dhindwal, D. N. Patil, P. Kumar

Date :   12 Feb 11 (Deposition) - 31 Aug 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Oxidoreductase, Short Chain Dehydrogenase, Sdr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dhindwal, D. N. Patil, M. Mohammadi, M. Sylvestre, S. Tomar, P. Kuma
Biochemical Studies And Ligand-Bound Structures Of Biphenyl Dehydrogenase From Pandoraea Pnomenusa Strain B-356 Reveal Basis For Broad Specificity Of The Enzyme.
J. Biol. Chem. V. 286 37011 2011
PubMed-ID: 21880718 | Reference-DOI: 10.1074/JBC.M111.291013
(for further references see the PDB file header)

Molecule 1 - CIS-2,3-DIHYDROBIPHENYL-2,3-DIOL DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.3.1.56
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET14B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	COMAMONAS TESTOSTERONI
	Organism Taxid	:	285
	Strain	:	B-356
	Synonym	:	2,3-DIHYDRO-2,3-DIHYDROXYBIPHENYL DEHYDROGENASE, 2,3-DIHYDROXY-4-PHENYLHEXA-4,6-DIENE DEHYDROGENASE, B2,3D, BIPHENYL-2,3-DIHYDRO-2,3-DIOL DEHYDROGENASE, BIPHENYL-CIS-DIOL DEHYDROGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , SER A:15 , GLY A:16 , LEU A:17 , ASP A:36 , LYS A:37 , GLY A:58 , ASP A:59 , VAL A:60 , ARG A:61 , ASN A:86 , GLY A:88 , ILE A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:184 , MET A:187 , THR A:189 , ASP A:190 , LEU A:191 , HOH A:2115	BINDING SITE FOR RESIDUE NAD A1276
2	AC2	SOFTWARE	GLY B:12 , SER B:15 , GLY B:16 , LEU B:17 , ASP B:36 , LYS B:37 , GLY B:58 , ASP B:59 , VAL B:60 , ASN B:86 , GLY B:88 , ILE B:141 , SER B:142 , TYR B:155 , LYS B:159 , PRO B:184 , MET B:187 , THR B:189 , ASP B:190 , LEU B:191 , ARG B:192 , HOH B:2006 , HOH B:2098	BINDING SITE FOR RESIDUE NAD B1276

(no "SS Bond" information available for 2Y99)

Asymmetric Unit

No.	Residues
1	Ala A:174	-	Pro A:175
2	Ala B:174	-	Pro B:175

(no "SAP(SNP)/Variant" information available for 2Y99)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	BPHB_COMTE	142-170	2	A:142-170 B:142-170

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	BPHB_COMTE	142-170	4	A:142-170 B:142-170

(no "Exon" information available for 2Y99)

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:267
 aligned with BPHB_COMTE | Q46381 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
           BPHB_COMTE     1 MKLTGEVALITGGASGLGRALVDRFVAEGARVAVLDKSAERLRELEVAHGGNAVGVVGDVRSLQDQKRAAERCLAAFGKIDTLIPNAGIWDYSTALADLPEDKIDAAFDDIFHVNVKGYIHAVKACLPALVSSRGSVVFTISNAGFYPNGGGPLYTATKHAVVGLVRQMAFELAPHVRVNGVAPGGMNTDLRGPSSLGLSEQSISSVPLADMLKSVLPIGRMPALEEYTGAYVFFATRGDSLPATGALLNYDGGMGVRGFLTAAGGADLPEKLNI 275
               SCOP domains d2y99a_ A: automated matches                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eee..........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..............--------.hhhhhhhh........hhhhhhhhhhhhhh..........eeee..hhhhh.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:142-170    --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y99 A   1 MKLTGEVALITGGASGLGRALVDRFVAEGARVAVLDKSAERLRELEVAHGGNAVGVVGDVRSLQDQKRAAERCLAAFGKIDTLIPNAGIWDYSTALADLPEDKIDAAFDDIFHVNVKGYIHAVKACLPALVSSRGSVVFTISNAGFYPNGGGPLYTATKHAVVGLVRQMAFELAPHVRVNGVAPGGMNTDLRGPSSLG--------VPLADMLKSVLPIGRMPALEEYTGAYVFFATRGDSLPATGALLNYDGGMGVRGFLTAAGGADLPEKLNI 275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       | -      |210       220       230       240       250       260       270     
                                                                                                                                                                                                                               198      207

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with BPHB_COMTE | Q46381 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270      
           BPHB_COMTE     1 MKLTGEVALITGGASGLGRALVDRFVAEGARVAVLDKSAERLRELEVAHGGNAVGVVGDVRSLQDQKRAAERCLAAFGKIDTLIPNAGIWDYSTALADLPEDKIDAAFDDIFHVNVKGYIHAVKACLPALVSSRGSVVFTISNAGFYPNGGGPLYTATKHAVVGLVRQMAFELAPHVRVNGVAPGGMNTDLRGPSSLGLSEQSISSVPLADMLKSVLPIGRMPALEEYTGAYVFFATRGDSLPATGALLNYDGGMGVRGFLTAAGGADLPEKLNIN 276
               SCOP domains d2y99b_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eee..........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee..............--------..hhhhhhhhh......hhhhhhhhhhhhhhhhhhh.....eeee..hhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:142-170    ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y99 B   1 MKLTGEVALITGGASGLGRALVDRFVAEGARVAVLDKSAERLRELEVAHGGNAVGVVGDVRSLQDQKRAAERCLAAFGKIDTLIPNAGIWDYSTALADLPEDKIDAAFDDIFHVNVKGYIHAVKACLPALVSSRGSVVFTISNAGFYPNGGGPLYTATKHAVVGLVRQMAFELAPHVRVNGVAPGGMNTDLRGPSSLG--------VPLADMLKSVLPIGRMPALEEYTGAYVFFATRGDSLPATGALLNYDGGMGVRGFLTAAGGADLPEKLNIN 276
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       | -      |210       220       230       240       250       260       270      
                                                                                                                                                                                                                               198      207

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: automated matches (114)

Comamonas testosteroni [TaxId: 285] (3)

1a	d2y99a_	A:
1b	d2y99b_	B:

(no "CATH Domain" information available for 2Y99)

(no "Pfam Domain" information available for 2Y99)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BPHB_COMTE | Q46381)

molecular function
	GO:0018509	cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase activity	Catalysis of the reaction: cis-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+ = biphenyl-2,3-diol + NADH + H+.
	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:0016628	oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
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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	Ligands, Modified Residues, Ions
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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:174 - Pro A:175	[ RasMol ]
		Ala B:174 - Pro B:175	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2y99
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	BPHB_COMTE \| Q46381
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	1.3.1.56
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		Disease Information	:	OMIM

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	BPHB_COMTE \| Q46381
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UniProtKB/Swiss-Prot
	BPHB_COMTE \| Q46381	:	2y93 3zv3 3zv4 3zv5 3zv6

2y93	CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B -356.
3zv3	CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3-DEHYDROGENASE (BPHB)FROM PANDORAEA PNOMENUSA STRAIN B -356 IN INTERMEDIATE STATE OF SUBSTRATE BINDING LOOP
3zv4	CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B -356 IN APO FORM AT 1.8 ANGSTROM
3zv5	CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B -356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT 2,3- DIHYDROXYBIPHENYL
3zv6	CRYSTAL STRUCTURE OF CIS-BIPHENYL-2,3-DIHYDRODIOL-2, 3-DEHYDROGENASE (BPHB) FROM PANDORAEA PNOMENUSA STRAIN B -356 COMPLEX WITH CO-ENZYME NAD AND PRODUCT ANALOG 4,4'-DIHYDROXYBIPHENYL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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