1DXY - JenaLib

Title :   STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE

Authors :   U. Dengler, K. Niefind, M. Kiess, D. Schomburg

Date :   13 Aug 96 (Deposition) - 16 Jun 97 (Release) - 15 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)
Biol. Unit 2: A  (6x)

Keywords :   D-2-Hydroxycarboxylate Dehydrogenase, D-Lactate Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. Dengler, K. Niefind, M. Kiess, D. Schomburg
Crystal Structure Of A Ternary Complex Of D-2-Hydroxyisocaproate Dehydrogenase From Lactobacillus Casei, Nad+ And 2-Oxoisocaproate At 1. 9 A Resolution.
J. Mol. Biol. V. 267 640 1997
PubMed-ID: 9126843 | Reference-DOI: 10.1006/JMBI.1996.0864
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:76 , VAL A:77 , GLY A:78 , TYR A:100 , ARG A:234 , COI A:404	BINDING SITE FOR RESIDUE SO4 A 338
2	AC2	SOFTWARE	PRO A:98 , ALA A:99 , PHE A:310 , HIS A:314 , THR A:326 , HOH A:653	BINDING SITE FOR RESIDUE SO4 A 339
3	AC3	SOFTWARE	TYR A:100 , GLY A:152 , GLY A:154 , HIS A:155 , ILE A:156 , TYR A:174 , ASP A:175 , PRO A:176 , HIS A:204 , VAL A:205 , PRO A:206 , ASN A:211 , ILE A:214 , THR A:232 , ALA A:233 , ARG A:234 , ASP A:258 , THR A:259 , HIS A:295 , TYR A:298 , COI A:404 , HOH A:502 , HOH A:504 , HOH A:580 , HOH A:581 , HOH A:629	BINDING SITE FOR RESIDUE NAD A 336
4	AC4	SOFTWARE	VAL A:77 , TYR A:100 , ARG A:234 , HIS A:295 , MET A:307 , NAD A:403 , SO4 A:401	BINDING SITE FOR RESIDUE COI A 337
5	CAT	UNKNOWN	VAL A:77 , GLY A:78 , TYR A:100 , THR A:232 , ARG A:234 , GLU A:263 , HIS A:295	ACTIVE SITE.

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	DHD2_LACPA	148-175	1	A:148-175
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	DHD2_LACPA	194-216	1	A:194-216
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	DHD2_LACPA	223-239	1	A:223-239

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	DHD2_LACPA	148-175	2	A:148-175
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	DHD2_LACPA	194-216	2	A:194-216
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	DHD2_LACPA	223-239	2	A:223-239

Biological Unit 2 (3, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	D_2_HYDROXYACID_DH_1	PS00065	D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.	DHD2_LACPA	148-175	6	A:148-175
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	DHD2_LACPA	194-216	6	A:194-216
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	DHD2_LACPA	223-239	6	A:223-239

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:330
 aligned with DHD2_LACPA | P17584 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:330
                                    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       280       290       300       310       320       330
           DHD2_LACPA     1 MKIIAYGARVDEIQYFKQWAKDTGNTLEYHTEFLDENTVEWAKGFDGINSLQTTPYAAGVFEKMHAYGIKFLTIRNVGTDNIDMTAMKQYGIRLSNVPAYSPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGTFIGKELGQQTVGVMGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDHPDFDYVSLEDLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYETEDLLNLAKHGSFKDPLWDELLGMPNVVLSPHIAYYTETAVHNMVYFSLQHLVDFLTKGETSTEVTG 330
               SCOP domains d1dxya2 A:1-100,A:300-330 D-2-hydroxyisocaproate dehydrogenase                                      d1dxya1 A:101-299 D-2-hydroxyisocaproate dehydrogenase                                                                                                                                                 d1dxya2 A:1-100,A:300-330       SCOP domains
               CATH domains 1dxyA01 A:1-101,A:299-330 NAD(P)-binding Rossmann-like Domain                                        1dxyA02 A:102-297 NAD(P)-binding Rossmann-like Domain                                                                                                                                               -1dxyA01 A:1-101,A:299-330        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh..eeee........hhhhh....eeee.......hhhhhhhhhh...eeee.........hhhhhh...eee......hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhh......hhh.eeeee...hhhhhhhhhhhhh..eeeee................hhhhhhh..eeee.....hhh.....hhhhhh....eeeee........hhhhhhhhh...eeeeee.....hhhhhhhhhhh.....hhhhhhh....eee........hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        ------------------D_2_HYDROXYACID_DH_2   ------D_2_HYDROXYACID_D------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dxy A   1 MKIIAYGARVDEIQYFKQWAKDTGNTLEYHTEFLDENTVEWAKGFDGINSLQTTPYAAGVFEKMHAYGIKFLTIRNVGTDNIDMTAMKQYGIRLSNVPAYSPAAIAEFALTDTLYLLRNMGKVQAQLQAGDYEKAGTFIGKELGQQTVGVMGTGHIGQVAIKLFKGFGAKVIAYDPYPMKGDHPDFDYVSLEDLFKQSDVIDLHVPGIEQNTHIINEAAFNLMKPGAIVINTARPNLIDTQAMLSNLKSGKLAGVGIDTYEYETEDLLNLAKHGSFKDPLWDELLGMPNVVLSPHIAYYTETAVHNMVYFSLQHLVDFLTKGETSTEVTG 330
                                    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       280       290       300       310       320       330

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 (2, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric Unit(hide GO term definitions)

Chain A (DHD2_LACPA | P17584)

molecular function
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, 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.
	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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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