2DLD - JenaLib

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Title :   D-LACTATE DEHYDROGENASE COMPLEXED WITH NADH AND OXAMATE

Authors :   C. R. Dunn, J. J. Holbrook

Date :   28 Oct 95 (Deposition) - 14 Mar 96 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Oxidoreductase (Choh(D)-Nad+(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Bernard, J. Delcour, A. Alvarez, A. Cortes, C. Willis, J. J. Holbroo
Dehydrogenases Engineering To Correct Substrate Inhibition In A Commercial Dehydrogenase
To Be Published
PubMed: search

Molecule 1 - D-LACTATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.28
	Organism Scientific	:	LACTOBACILLUS HELVETICUS
	Organism Taxid	:	1587
	Other Details	:	CRYSTALLIZED IN 11% PEG 4000, 5 MM BIS-TRIS PH 6.8, 75 MG/ML ENZYME, 3 MM NADH, 10 MM OXAMATE
	Synonym	:	R-LACTATE DEHYDROGENASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	NAI	2	Ligand/Ion	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2	OXM	2	Ligand/Ion	OXAMIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:154 , GLY A:155 , HIS A:156 , ILE A:157 , ASP A:176 , ILE A:177 , HIS A:206 , VAL A:207 , PRO A:208 , ASN A:213 , CYS A:234 , SER A:235 , ARG A:236 , THR A:261 , HIS A:297 , ALA A:299 , PHE A:337 , OXM A:402	BINDING SITE FOR RESIDUE NAI A 401
2	AC2	SOFTWARE	SER A:235 , ARG A:236 , HIS A:297 , NAI A:401	BINDING SITE FOR RESIDUE OXM A 402
3	AC3	SOFTWARE	THR B:154 , GLY B:155 , HIS B:156 , ILE B:157 , ASP B:176 , ILE B:177 , HIS B:206 , VAL B:207 , PRO B:208 , ASN B:213 , CYS B:234 , SER B:235 , ARG B:236 , ASP B:260 , THR B:261 , HIS B:297 , ALA B:299 , OXM B:402	BINDING SITE FOR RESIDUE NAI B 401
4	AC4	SOFTWARE	ARG B:236 , HIS B:297 , NAI B:401	BINDING SITE FOR RESIDUE OXM B 402

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:137	-	Pro A:138
2	Ala B:137	-	Pro B:138

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

Asymmetric/Biological Unit (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.	LDHD_LACHE	149-176	2	A:149-176 B:149-176
2	D_2_HYDROXYACID_DH_2	PS00670	D-isomer specific 2-hydroxyacid dehydrogenases signature 2.	LDHD_LACHE	196-218	2	A:196-218 B:196-218
3	D_2_HYDROXYACID_DH_3	PS00671	D-isomer specific 2-hydroxyacid dehydrogenases signature 3.	LDHD_LACHE	225-241	2	A:225-241 B:225-241

(no "Exon" information available for 2DLD)

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:337
 aligned with LDHD_LACHE | P30901 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:337
                                    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       
           LDHD_LACHE     1 MTKVFAYAIRKDEEPFLNEWKEAHKDIDVDYTDKLLTPETAKLAKGADGVVVYQQLDYTADTLQALADAGVTKMSLRNVGVDNIDMDKAKELGFQITNVPVYSPNAIAEHAAIQAARVLRQDKRMDEKMAKRDLRWAPTIGREVRDQVVGVVGTGHIGQVFMRIMEGFGAKVIAYDIFKNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDEVGVFNKDWEGKEFPDKRLADLIDRPNVLVTPHTAFYTTHAVRNMVVKAFNNNLKLINGEKPDSPVALNKNKF 337
               SCOP domains d2dlda2 A:1-103,A:301-337 D-lactate dehydrogenase                                                      d2dlda1 A:104-300 D-lactate dehydrogenase                                                                                                                                                            d2dlda2 A:1-103,A:301-337             SCOP domains
               CATH domains 2dldA01 A:1-103,A:301-336 NAD(P)-binding Rossmann-like Domain                                          2dldA02 A:104-299 NAD(P)-binding Rossmann-like Domain                                                                                                                                               -2dldA01 A:1-103,A:301-336           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhh....eee.........hhhh.....eeee.......hhhhhhhhhhh..eee..........hhhhhh.............hhhhhhhhhhhhhhhh.hhhhhhhhh.............hhh.eeeee...hhhhhhhhhhhhh..eeeee.......hhhh......hhhhhh...eeee.............hhhhhh....eeeee...hhh..hhhhhhhhhh..eeeeee.....hhhh............hhhhhhhh...eee........hhhhhhhhhhhhhhhhhhhh............... 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
                 2dld A   1 MTKVFAYAIRKDEEPFLNEWKEAHKDIDVDYTDKLLTPETAKLAKGADGVVVYQQLDYTADTLQALADAGVTKMSLRNVGVDNIDMDKAKELGFQITNVPVYSPNAIAEHAAIQAARVLRQDKRMDEKMAKRDLRWAPTIGREVRDQVVGVVGTGHIGQVFMRIMEGFGAKVIAYDIFKNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDEVGVFNKDWEGKEFPDKRLADLIDRPNVLVTPHTAFYTTHAVRNMVVKAFNNNLKLINGEKPDSPVALNKNKF 337
                                    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

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with LDHD_LACHE | P30901 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:337
                                    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       
           LDHD_LACHE     1 MTKVFAYAIRKDEEPFLNEWKEAHKDIDVDYTDKLLTPETAKLAKGADGVVVYQQLDYTADTLQALADAGVTKMSLRNVGVDNIDMDKAKELGFQITNVPVYSPNAIAEHAAIQAARVLRQDKRMDEKMAKRDLRWAPTIGREVRDQVVGVVGTGHIGQVFMRIMEGFGAKVIAYDIFKNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDEVGVFNKDWEGKEFPDKRLADLIDRPNVLVTPHTAFYTTHAVRNMVVKAFNNNLKLINGEKPDSPVALNKNKF 337
               SCOP domains d2dldb2 B:1-103,B:301-337 D-lactate dehydrogenase                                                      d2dldb1 B:104-300 D-lactate dehydrogenase                                                                                                                                                            d2dldb2 B:1-103,B:301-337             SCOP domains
               CATH domains 2dldB01 B:1-103,B:301-336 NAD(P)-binding Rossmann-like Domain                                          2dldB02 B:104-299 NAD(P)-binding Rossmann-like Domain                                                                                                                                               -2dldB01 B:1-103,B:301-336           - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhh......eeeee.....hhhhh......eeee.........hhhhhhhhh..eeee.........hhhhhhh..eee......hhhhhhhhhhhhhhhhh.hhhhhhhhhh............hhh.eeeee...hhhhhhhhhhhhh..eeeee.....hhhhhh......hhhhhh...eeee.............hhhhhh....eeeee........hhhhhhhhhh..eeeeee...hhh...............hhhhhhh....eee........hhhhhhhhhhhhhhhhhhhh............... 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
                 2dld B   1 MTKVFAYAIRKDEEPFLNEWKEAHKDIDVDYTDKLLTPETAKLAKGADGVVVYQQLDYTADTLQALADAGVTKMSLRNVGVDNIDMDKAKELGFQITNVPVYSPNAIAEHAAIQAARVLRQDKRMDEKMAKRDLRWAPTIGREVRDQVVGVVGTGHIGQVFMRIMEGFGAKVIAYDIFKNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDKSIAEMKDGVVIVNCSRGRLVDTDAVIRGLDSGKIFGFVMDTYEDEVGVFNKDWEGKEFPDKRLADLIDRPNVLVTPHTAFYTTHAVRNMVVKAFNNNLKLINGEKPDSPVALNKNKF 337
                                    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 '\|'

Asymmetric/Biological 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)

Lactobacillus helveticus. Organism_taxid: 1587 (1)

1a	2dldA02	A:104-299
1b	2dldB02	B:104-299
1c	2dldA01	A:1-103,A:301-336
1d	2dldB01	B:1-103,B:301-336

(no "Pfam Domain" information available for 2DLD)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LDHD_LACHE | P30901)

molecular function
	GO:0008720	D-lactate dehydrogenase activity	Catalysis of the reaction: (R)-lactate + NAD(+) = H(+) + NADH + pyruvate.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:137 - Pro A:138	[ RasMol ]
		Ala B:137 - Pro B:138	[ RasMol ]

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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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