2Q2V - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM PSEUDOMONAS PUTIDA

Authors :   K. S. Paithankar, C. Feller, E. B. Kuettner, A. Keim, M. Grunow, N. Strat

Date :   29 May 07 (Deposition) - 30 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4: C,D  (2x)

Keywords :   D-3-Hydroxybutyrate Dehydrogenase, Pseudomonas Putida, Sdr, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Paithankar, C. Feller, E. B. Kuettner, A. Keim, M. Grunow, N. Strater
Cosubstrate-Induced Dynamics Of D-3-Hydroxybutyrate Dehydrogenase From Pseudomonas Putida.
Febs J. V. 274 5767 2007
PubMed-ID: 17958702 | Reference-DOI: 10.1111/J.1742-4658.2007.06102.X

Molecule 1 - BETA-D-HYDROXYBUTYRATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BDHA
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 4 (2x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Biological Unit 3 (1, 1)

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

Biological Unit 4 (1, 4)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:12 , THR B:14 , SER B:15 , GLY B:16 , ILE B:17 , ASN B:35 , GLY B:36 , PHE B:37 , ALA B:59 , ASP B:60 , LEU B:61 , ASN B:87 , GLY B:89 , LYS B:106 , LEU B:110 , ALA B:138 , SER B:139 , TYR B:152 , LYS B:156 , PRO B:182 , GLY B:183 , TRP B:184 , VAL B:185 , THR B:187 , PRO B:188 , LEU B:189 , VAL B:190 , HOH B:313 , HOH B:350	BINDING SITE FOR RESIDUE NAD B 300
2	AC2	SOFTWARE	GLY C:12 , THR C:14 , SER C:15 , GLY C:16 , ILE C:17 , ASN C:35 , GLY C:36 , PHE C:37 , ALA C:59 , ASP C:60 , LEU C:61 , ASN C:87 , ALA C:88 , GLY C:89 , LEU C:110 , ILE C:137 , ALA C:138 , SER C:139 , TYR C:152 , LYS C:156 , PRO C:182 , GLY C:183 , TRP C:184 , VAL C:185 , THR C:187 , PRO C:188 , VAL C:190 , HOH C:330 , HOH C:350 , HOH C:355	BINDING SITE FOR RESIDUE NAD C 300
3	AC3	SOFTWARE	GLU A:102 , GLY D:12 , THR D:14 , SER D:15 , GLY D:16 , ILE D:17 , ASN D:35 , PHE D:37 , ALA D:59 , ASP D:60 , LEU D:61 , ASN D:87 , ALA D:88 , GLY D:89 , LEU D:110 , ILE D:137 , ALA D:138 , SER D:139 , TYR D:152 , LYS D:156 , PRO D:182 , GLY D:183 , TRP D:184 , VAL D:185 , THR D:187 , LEU D:189 , VAL D:190 , HOH D:311 , HOH D:350	BINDING SITE FOR RESIDUE NAD D 300

(no "SS Bond" information available for 2Q2V)

(no "Cis Peptide Bond" information available for 2Q2V)

(no "SAP(SNP)/Variant" information available for 2Q2V)

(no "PROSITE Motif" information available for 2Q2V)

(no "Exon" information available for 2Q2V)

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:255
 aligned with Q9AE70_PSEPU | Q9AE70 from UniProtKB/TrEMBL  Length:256

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9AE70_PSEPU     2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDRAANGGDPLQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
               SCOP domains d2q2va_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2q2vA00 A:2-256 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhh..hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2v A   2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDRAANGGDPLQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with Q9AE70_PSEPU | Q9AE70 from UniProtKB/TrEMBL  Length:256

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9AE70_PSEPU     2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDRAANGGDPLQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
               SCOP domains d2q2vb_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2q2vB00 B:2-256 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhh--.hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2v B   2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDRAA--GDPLQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       | -|      211       221       231       241       251     
                                                                                                                                                                                                                               199  |                                                      
                                                                                                                                                                                                                                  202

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with Q9AE70_PSEPU | Q9AE70 from UniProtKB/TrEMBL  Length:256

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9AE70_PSEPU     2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDRAANGGDPLQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
               SCOP domains d2q2vc_ C: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2q2vC00 C:2-256 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhh.-------hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2v C   2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDR-------LQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     |   -   |   211       221       231       241       251     
                                                                                                                                                                                                                             197     205

Chain D from PDB  Type:PROTEIN  Length:247
 aligned with Q9AE70_PSEPU | Q9AE70 from UniProtKB/TrEMBL  Length:256

    Alignment length:255
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251     
         Q9AE70_PSEPU     2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDRAANGGDPLQAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
               SCOP domains d2q2vd_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2q2vD00 D:2-256 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----adh_short-2q2vD01 D:6-171                                                                                                                                             ------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----adh_short-2q2vD02 D:6-171                                                                                                                                             ------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----adh_short-2q2vD03 D:6-171                                                                                                                                             ------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----adh_short-2q2vD04 D:6-171                                                                                                                                             ------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhh.hhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhh--------hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q2v D   2 TLKGKTALVTGSTSGIGLGIAQVLARAGANIVLNGFGDPAPALAEIARHGVKAVHHPADLSDVAQIEALFALAEREFGGVDILVNNAGIQHVAPVEQFPLESWDKIIALNLSAVFHGTRLALPGMRARNWGRIINIASVHGLVGSTGKAAYVAAKHGVVGLTKVVGLETATSNVTCNAICPGWVLTPLVQKQIDDR--------QAQHDLLAEKQPSLAFVTPEHLGELVLFLCSEAGSQVRGAAWNVDGGWLAQ 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     |   -    |  211       221       231       241       251     
                                                                                                                                                                                                                             197      206

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) (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)

Pseudomonas putida [TaxId: 303] (3)

1a	d2q2va_	A:
1b	d2q2vb_	B:
1c	d2q2vc_	C:
1d	d2q2vd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Pseudomonas putida. Organism_taxid: 303. (5)

1a	2q2vD00	D:2-256
1b	2q2vA00	A:2-256
1c	2q2vC00	C:2-256
1d	2q2vB00	B:2-256

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Pseudomonas putida (Arthrobacter siderocapsulatus) (3)

1a	adh_short-2q2vD01	D:6-171
1b	adh_short-2q2vD02	D:6-171
1c	adh_short-2q2vD03	D:6-171
1d	adh_short-2q2vD04	D:6-171

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9AE70_PSEPU | Q9AE70)

molecular function
	GO:0003858	3-hydroxybutyrate dehydrogenase activity	Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + H(+) + NADH.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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: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 Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2q2v)

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	2q2v
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	Q9AE70_PSEPU \| Q9AE70	:	2q2q 2q2w

Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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