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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF ALCALIGENES FAECALIS D-3-HYDROXYBUTYRATE DEHYDROGENASE IN COMPLEX WITH NAD(+) AND ACETATE

Authors :   M. M. Hoque, S. Shimizu, M. T. Hossain, T. Yamamoto, K. Suzuki, A. Takena

Date :   06 Jan 12 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Nad Dependent Enzyme, Hydroxybutyrate Dehydrogenase, Ketone Bodies, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Hoque, S. Shimizu, M. T. Hossain, T. Yamamoto, S. Imamura, K. Suzuki, M. Tsunoda, H. Amano, T. Sekiguchi, A. Takenaka
The Structures Of Alcaligenes Faecalis D-3-Hydroxybutyrate Dehydrogenase Before And After Nad+ And Acetate Binding Suggest A Dynamical Reaction Mechanism As A Member Of The Sdr Family.
Acta Crystallogr. , Sect. D V. 64 496 2008
PubMed-ID: 18453685 | Reference-DOI: 10.1107/S0907444908004009

Molecule 1 - D-3-HYDROXYBUTYRATE DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.30
	Organism Scientific	:	ALCALIGENES FAECALIS
	Organism Taxid	:	511

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 14)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	CL	4	Ligand/Ion	CHLORIDE ION
4	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:94 , HIS A:144 , LYS A:152 , TRP A:187 , LEU A:192 , GLN A:196 , HOH A:403	BINDING SITE FOR RESIDUE ACT A 301
02	AC2	SOFTWARE	SER A:149 , VAL A:150 , LYS A:219	BINDING SITE FOR RESIDUE CL A 302
03	AC3	SOFTWARE	GLY A:11 , THR A:13 , SER A:14 , ILE A:16 , PHE A:36 , ASP A:63 , LEU A:64 , ASN A:90 , ALA A:91 , GLY A:92 , LEU A:113 , ILE A:140 , ALA A:141 , SER A:142 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , TRP A:187 , VAL A:188 , THR A:190 , PRO A:191 , LEU A:192 , VAL A:193 , HOH A:402 , HOH A:403 , HOH A:465 , HOH A:596 , HOH C:486 , HOH C:603	BINDING SITE FOR RESIDUE NAD A 303
04	AC4	SOFTWARE	GLN B:94 , HIS B:144 , LYS B:152 , TRP B:187 , LEU B:192 , GLN B:196 , NAD B:303 , HOH B:517	BINDING SITE FOR RESIDUE ACT B 301
05	AC5	SOFTWARE	SER B:149 , VAL B:150 , LYS B:219	BINDING SITE FOR RESIDUE CL B 302
06	AC6	SOFTWARE	GLY B:11 , THR B:13 , SER B:14 , GLY B:15 , ILE B:16 , ASN B:34 , PHE B:36 , ASP B:63 , LEU B:64 , ASN B:90 , ALA B:91 , GLY B:92 , ILE B:140 , ALA B:141 , SER B:142 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , TRP B:187 , VAL B:188 , THR B:190 , PRO B:191 , LEU B:192 , VAL B:193 , ACT B:301 , HOH B:405 , HOH B:474 , HOH B:517 , HOH B:531 , HOH B:544 , HOH B:548 , HOH B:553	BINDING SITE FOR RESIDUE NAD B 303
07	AC7	SOFTWARE	ARG B:260 , HOH B:451 , HOH B:482 , ARG D:260 , HOH D:1001 , HOH D:1053	BINDING SITE FOR RESIDUE CA B 304
08	AC8	SOFTWARE	VAL A:147 , ARG A:260 , HOH A:473 , ARG C:260 , HOH C:435 , HOH C:463 , HOH C:467	BINDING SITE FOR RESIDUE CA C 301
09	AC9	SOFTWARE	GLN C:94 , HIS C:144 , LYS C:152 , TRP C:187 , LEU C:192 , GLN C:196 , NAD C:304 , HOH C:459	BINDING SITE FOR RESIDUE ACT C 302
10	BC1	SOFTWARE	SER C:149 , VAL C:150 , LYS C:219	BINDING SITE FOR RESIDUE CL C 303
11	BC2	SOFTWARE	HOH A:534 , GLY C:11 , THR C:13 , SER C:14 , ILE C:16 , PHE C:36 , ASP C:63 , LEU C:64 , ASN C:90 , ALA C:91 , GLY C:92 , LEU C:113 , ILE C:140 , ALA C:141 , SER C:142 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , TRP C:187 , VAL C:188 , THR C:190 , PRO C:191 , LEU C:192 , VAL C:193 , ACT C:302 , HOH C:441 , HOH C:510 , HOH C:598 , HOH C:599 , HOH C:602	BINDING SITE FOR RESIDUE NAD C 304
12	BC3	SOFTWARE	GLN D:94 , HIS D:144 , LYS D:152 , TRP D:187 , GLN D:196 , HOH D:1019	BINDING SITE FOR RESIDUE ACT D 301
13	BC4	SOFTWARE	SER D:149 , VAL D:150 , LYS D:219	BINDING SITE FOR RESIDUE CL D 302
14	BC5	SOFTWARE	GLY D:11 , THR D:13 , SER D:14 , GLY D:15 , ILE D:16 , ASN D:34 , PHE D:36 , ASP D:63 , LEU D:64 , ASN D:90 , ALA D:91 , GLY D:92 , ILE D:140 , ALA D:141 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , TRP D:187 , VAL D:188 , THR D:190 , PRO D:191 , LEU D:192 , VAL D:193 , HOH D:1019 , HOH D:1117 , HOH D:1126 , HOH D:1187 , HOH D:1188 , HOH D:1195	BINDING SITE FOR RESIDUE NAD D 303

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

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

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

(no "PROSITE Motif" information available for 3VDQ)

(no "Exon" information available for 3VDQ)

Asymmetric/Biological 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:260
 aligned with D0VWQ0_ALCFA | D0VWQ0 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         D0VWQ0_ALCFA     1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
               SCOP domains d3vdqa_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vdq A   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
                                    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

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with D0VWQ0_ALCFA | D0VWQ0 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         D0VWQ0_ALCFA     1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
               SCOP domains d3vdqb_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vdq B   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
                                    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

Chain C from PDB  Type:PROTEIN  Length:260
 aligned with D0VWQ0_ALCFA | D0VWQ0 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         D0VWQ0_ALCFA     1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
               SCOP domains d3vdqc_ C: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vdq C   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
                                    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

Chain D from PDB  Type:PROTEIN  Length:260
 aligned with D0VWQ0_ALCFA | D0VWQ0 from UniProtKB/TrEMBL  Length:260

    Alignment length:260
                                    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
         D0VWQ0_ALCFA     1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
               SCOP domains d3vdqd_ D: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vdq D   1 MLKGKKAVVTGSTSGIGLAMATELAKAGADVVINGFGQPEDIERERSTLESKFGVKAYYLNADLSDAQATRDFIAKAAEALGGLDILVNNAGIQHTAPIEEFPVDKWNAIIALNLSAVFHGTAAALPIMQKQGWGRIINIASAHGLVASVNKSAYVAAKHGVVGLTKVTALENAGKGITCNAICPGWVRTPLVEKQIEAISQQKGIDIEAAARELLAEKQPSLQFVTPEQLGGAAVFLSSAAADQMTGTTLSLDGGWTAR 260
                                    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

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/Biological 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)

Alcaligenes faecalis [TaxId: 511] (6)

1a	d3vdqa_	A:
1b	d3vdqb_	B:
1c	d3vdqc_	C:
1d	d3vdqd_	D:

(no "CATH Domain" information available for 3VDQ, only for superseded entry 2ZEA replaced by 3VDQ)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (D0VWQ0_ALCFA | D0VWQ0)

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/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vdq)

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	1.1.1.30
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UniProtKB/TrEMBL
	D0VWQ0_ALCFA \| D0VWQ0	:	2yz7 3vdr 3w8d 3w8e 3w8f 5b4t 5b4u 5b4v

2yz7	D-3-HYDROXYBUTYRATE DEHYDROGENASE IN NATIVE FORM
3vdr

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0 ; only for superseded entry 2ZEA: 1,4)

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Gene Ontology (4, 4)

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