3V2H - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF D-BETA-HYDROXYBUTYRATE DEHYDROGENASE FROM SINORHIZOBIUM MELILOTI

Authors :   Z. Zhang, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar, J R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swaminathan, New Y Structural Genomics Research Consortium (Nysgrc)

Date :   12 Dec 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Zhang, S. C. Almo, S. Swaminathan
The Crystal Structure Of D-Beta-Hydroxybutyrate Dehydrogenase From Sinorhizobium Meliloti
To Be Published
PubMed: search

Molecule 1 - D-BETA-HYDROXYBUTYRATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BDHA, RB1136, SMB21010
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	266834
	Strain	:	1021
	Synonym	:	BDH, 3-HYDROXYBUTYRATE DEHYDROGENASE, 3-HBDH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 36)

No.	Name	Count	Type	Full Name
1	MSE	36	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3V2H)

(no "SS Bond" information available for 3V2H)

(no "Cis Peptide Bond" information available for 3V2H)

(no "SAP(SNP)/Variant" information available for 3V2H)

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.	BDHA_RHIME	140-168	2	A:140-168 B:140-168

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.	BDHA_RHIME	140-168	4	A:140-168 B:140-168

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	BDHA_RHIME	140-168	2	A:140-168 B:140-168

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	BDHA_RHIME	140-168	2	A:140-168 -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	BDHA_RHIME	140-168	2	- B:140-168

(no "Exon" information available for 3V2H)

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:232
 aligned with BDHA_RHIME | O86034 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:260
                              1                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
           BDHA_RHIME     - --MTKTAVITGSTSGIGLAIARTLAKAGANIVLNGFGAPDEIRTVTDEVAGLSSGTVLHHPADMTKPSEIADMMAMVADRFGGADILVNNAGVQFVEKIEDFPVEQWDRIIAVNLSSSFHTIRGAIPPMKKKGWGRIINIASAHGLVASPFKSAYVAAKHGIMGLTKTVALEVAESGVTVNSICPGYVLTPLVEKQIPDQARTRGITEEQVINEVMLKGQPTKKFITVEQVASLALYLAGDDAAQITGTHVSMDGGWTAQ 258
               SCOP domains d3v2ha_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....----------------------------........hhhhhhhhhhhhhhhhhhhh...eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:140-168    ------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v2h A  -1 SmmTKTAVITGSTSGIGLAIARTLAKAGANIVLNGFGAPDEIRTVTDEVAGLSSGTVLHHPADmTKPSEIADmmAmVADRFGGADILVNNAGVQFVEKIEDFPVEQWDRIIAVNLSSSFHTIRGAIPPmKKKGWGRIINIASAHGLVASPFKSAYVAAKHGImGLTKTVALEVAESGVTVNSICPGYVLT----------------------------GQPTKKFITVEQVASLALYLAGDDAAQITGTHVSmDGGWTAQ 258
                             ||      8        18        28        38        48        58   |    68  || |  78        88        98       108       118       128       138       148       158  |    168       178       188         -         -       218       228       238       248  |    258
                             ||                                                           62-MSE   71-MSE                                                 127-MSE                           161-MSE                    188                          217                               251-MSE   
                             0-MSE                                                                  72-MSE                                                                                                                                                                                      
                              1-MSE                                                                   74-MSE

Chain B from PDB  Type:PROTEIN  Length:231
 aligned with BDHA_RHIME | O86034 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:260
                              1                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258
           BDHA_RHIME     - --MTKTAVITGSTSGIGLAIARTLAKAGANIVLNGFGAPDEIRTVTDEVAGLSSGTVLHHPADMTKPSEIADMMAMVADRFGGADILVNNAGVQFVEKIEDFPVEQWDRIIAVNLSSSFHTIRGAIPPMKKKGWGRIINIASAHGLVASPFKSAYVAAKHGIMGLTKTVALEVAESGVTVNSICPGYVLTPLVEKQIPDQARTRGITEEQVINEVMLKGQPTKKFITVEQVASLALYLAGDDAAQITGTHVSMDGGWTAQ 258
               SCOP domains d3v2hb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....-----------------------------........hhhhhhhhhhhhhhhhhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:140-168    ------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v2h B  -1 SmmTKTAVITGSTSGIGLAIARTLAKAGANIVLNGFGAPDEIRTVTDEVAGLSSGTVLHHPADmTKPSEIADmmAmVADRFGGADILVNNAGVQFVEKIEDFPVEQWDRIIAVNLSSSFHTIRGAIPPmKKKGWGRIINIASAHGLVASPFKSAYVAAKHGImGLTKTVALEVAESGVTVNSICPGYVL-----------------------------GQPTKKFITVEQVASLALYLAGDDAAQITGTHVSmDGGWTAQ 258
                             ||      8        18        28        38        48        58   |    68  || |  78        88        98       108       118       128       138       148       158  |    168       178        |-         -         -       218       228       238       248  |    258
                             0-MSE                                                        62-MSE   71-MSE                                                 127-MSE                           161-MSE                   187                           217                               251-MSE   
                              1-MSE                                                                 72-MSE                                                                                                                                                                                      
                                                                                                      74-MSE

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: automated matches (447)

Protein domain: automated matches (447)

Sinorhizobium meliloti [TaxId: 266834] (11)

1a	d3v2ha_	A:
1b	d3v2hb_	B:

(no "CATH Domain" information available for 3V2H)

(no "Pfam Domain" information available for 3V2H)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BDHA_RHIME | O86034)

molecular function
	GO:0003858	3-hydroxybutyrate dehydrogenase activity	Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + H(+) + NADH.
	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.

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Biological Units
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