1X1T - JenaLib

Title :   CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE FROM PSEUDOMONAS FRAGI COMPLEXED WITH NAD+

Authors :   K. Ito, Y. Nakajima, E. Ichihara, K. Ogawa, T. Yoshimoto

Date :   13 Apr 05 (Deposition) - 10 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.52

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Nad, Nadh, Sdr, Short Chain Dehydrogenase, Ketone Body, Beta- Hydroxybutyrate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Ito, Y. Nakajima, E. Ichihara, K. Ogawa, N. Katayama, K. Nakashima, T. Yoshimoto
D-3-Hydroxybutyrate Dehydrogenase From Pseudomonas Fragi: Molecular Cloning Of The Enzyme Gene And Crystal Structure Of The Enzyme
J. Mol. Biol. V. 355 722 2006
PubMed-ID: 16325199 | Reference-DOI: 10.1016/J.JMB.2005.10.072

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:38 , HIS A:128 , HOH A:501 , HOH A:502	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	SER A:142 , HIS A:144 , LYS A:152 , TYR A:155 , TRP A:257 , NAD A:300 , HOH A:596	BINDING SITE FOR RESIDUE CAC A 302
3	AC3	SOFTWARE	GLY A:11 , THR A:13 , SER A:14 , GLY A:15 , ILE A:16 , GLY A:35 , PHE A:36 , ALA A:62 , 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 , CAC A:302 , HOH A:519 , HOH A:667 , HOH A:673	BINDING SITE FOR RESIDUE NAD A 300

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

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:236
 aligned with Q5KST5_PSEFR | Q5KST5 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
         Q5KST5_PSEFR     1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRTPLVEKQISALAEKNGVDQETAARELLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
               SCOP domains d1x1ta_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1x1tA00 A:1-260 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                  CATH domains
               Pfam domains ----adh_short-1x1tA01 A:5-174                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee....hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....------------------------hhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1t A   1 MLKGKVAVVTGSTSGIGLGIATALAAQGADIVLNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMGRIDILVNNAGIQHTALIEDFPTEKWDAILALNLSAVFHGTAAALPHMKKQGFGRIINIASAHGLVASANKSAYVAAKHGVVGFTKVTALETAGQGITANAICPGWVRT------------------------LLSEKQPSLQFVTPEQLGGTAVFLASDAAAQITGTTVSVDGGWTAR 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         -         -    |  220       230       240       250       260
                                                                                                                                                                                                                       190                      215

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A (Q5KST5_PSEFR | Q5KST5)

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.

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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
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Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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