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(-) Description

Title :  INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS
 
Authors :  A. Razeto, S. Kochhar, H. Hottinger, M. Dauter, K. S. Wilson, V. S. Lamzin
Date :  14 Aug 01  (Deposition) - 29 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nad-Dependent Dehydrogenase, Last Step Of Glycolysis Under Anaerobic Conditions, Reversible Interconversion Of Pyruvate Into D-Lactate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Razeto, S. Kochhar, H. Hottinger, M. Dauter, K. S. Wilson, V. S. Lamzin
Domain Closure, Substrate Specificity And Catalysis Of D-Lactate Dehydrogenase From Lactobacillus Bulgaricus.
J. Mol. Biol. V. 318 109 2002
PubMed-ID: 12054772  |  Reference-DOI: 10.1016/S0022-2836(02)00086-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-LACTATE DEHYDROGENASE
    Cellular Location: CYTOPLASM
    Chains: A, B
    EC Number: 1.1.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Gene: LDHA
    Expression System Plasmid: PKBULDH
    Expression System Strain: SURE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LDHA
    Organism Scientific: LACTOBACILLUS DELBRUECKII SUBSP. BULGARICUS
    Organism Taxid: 1585
    Other Details: NESTLE CULTURE COLLECTION. PCR AMPLIFIED LDHA GENE
    Strain: N42
    Synonym: D-LDH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:78 , VAL B:79 , GLY B:80 , TYR B:102 , ARG B:236 , HIS B:297 , NAD B:360 , HOH B:422BINDING SITE FOR RESIDUE SO4 B 341
2AC2SOFTWARETYR A:102 , ILE A:107 , GLY A:153 , GLY A:155 , HIS A:156 , ILE A:157 , TYR A:175 , ASP A:176 , ILE A:177 , HIS A:206 , VAL A:207 , PRO A:208 , ASN A:213 , VAL A:234 , SER A:235 , ARG A:236 , ASP A:260 , HIS A:297 , ALA A:299 , PHE A:300 , HOH A:390 , HOH A:428 , HOH A:463 , HOH A:470 , HOH A:485 , HOH A:487BINDING SITE FOR RESIDUE NAD A 350
3AC3SOFTWARETYR B:102 , ILE B:107 , GLY B:155 , HIS B:156 , ILE B:157 , TYR B:175 , ASP B:176 , ILE B:177 , HIS B:206 , VAL B:207 , PRO B:208 , ASN B:213 , VAL B:234 , SER B:235 , ARG B:236 , ASP B:260 , HIS B:297 , ALA B:299 , PHE B:300 , SO4 B:341 , HOH B:376 , HOH B:379 , HOH B:382 , HOH B:386 , HOH B:395 , HOH B:453BINDING SITE FOR RESIDUE NAD B 360

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J49)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:137 -Pro A:138
2Ala B:137 -Pro B:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J49)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_2_HYDROXYACID_DH_1PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.LDHD_LACDA149-176
 		  2A:149-176
B:149-176
2D_2_HYDROXYACID_DH_2PS00670 D-isomer specific 2-hydroxyacid dehydrogenases signature 2.LDHD_LACDA196-218
 		  2A:196-218
B:196-218
3D_2_HYDROXYACID_DH_3PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.LDHD_LACDA225-241
 		  2A:225-241
B:225-241

(-) Exons   (0, 0)

(no "Exon" information available for 1J49)

(-) Sequences/Alignments

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:332
 aligned with LDHD_LACDA | P26297 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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_LACDA     1 MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGVVVYQQLDYTAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAPTIGREVRDQVVGVIGTGHIGQVFMQIMEGFGAKVIAYDIFRNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAFYTTHAVRNMVVKAFDNNLELVEGKEAETPVKV 332
               SCOP domains d1j49a2 A:1-103,A:301-332 D-lactate dehydrogenase                                                      d1j49a1 A:104-300 D-lactate dehydrogenase                                                                                                                                                            d1j49a2 A:1-103,A:301-332        SCOP domains
               CATH domains 1j49A01 A:1-103,A:301-332 NAD(P)-binding Rossmann-like Domain                                          1j49A02 A:104-299 NAD(P)-binding Rossmann-like Domain                                                                                                                                               -1j49A01 A:1-103,A:301-332        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhh....eeee........hhhhhh...eeee......hhhhhhhhhh....eeee........hhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhh.eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhh....hhhhhhhhh.eeee............hhhhhhhh...eeeee..hhhhhhhhhhhhhhhh..eeeeee....................hhhhhhhhhh..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
                 1j49 A   1 MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGVVVYQQLDYIAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAPTIGREVRDQVVGVVGTGHIGQVFMQIMEGFGAKVITYDIFRNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAFYTTHAVRNMVVKAFDNNLELVEGKEAETPVKV 332
                                    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:332
 aligned with LDHD_LACDA | P26297 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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_LACDA     1 MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGVVVYQQLDYTAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAPTIGREVRDQVVGVIGTGHIGQVFMQIMEGFGAKVIAYDIFRNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAFYTTHAVRNMVVKAFDNNLELVEGKEAETPVKV 332
               SCOP domains d1j49b2 B:1-103,B:301-332 D-lactate dehydrogenase                                                      d1j49b1 B:104-300 D-lactate dehydrogenase                                                                                                                                                            d1j49b2 B:1-103,B:301-332        SCOP domains
               CATH domains 1j49B01 B:1-103,B:301-332 NAD(P)-binding Rossmann-like Domain                                          1j49B02 B:104-299 NAD(P)-binding Rossmann-like Domain                                                                                                                                               -1j49B01 B:1-103,B:301-332        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhh.....eeee.....hhhhhhhhh...eeee......hhhhhhhhhh....eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhh.eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhh....hhhhhhhhh.eeee....hhhhh...hhhhhhh....eeeee..hhhhhhhhhhhhhhhh..eeeeee....................hhhhhhhhhh..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
                 1j49 B   1 MTKIFAYAIREDEKPFLKEWEDAHKDVEVEYTDKLLTPETVALAKGADGVVVYQQLDYIAETLQALADNGITKMSLRNVGVDNIDMAKAKELGFQITNVPVYSPNAIAEHAAIQAARILRQDKAMDEKVARHDLRWAPTIGREVRDQVVGVVGTGHIGQVFMQIMEGFGAKVITYDIFRNPELEKKGYYVDSLDDLYKQADVISLHVPDVPANVHMINDESIAKMKQDVVIVNVSRGPLVDTDAVIRGLDSGKIFGYAMDVYEGEVGIFNEDWEGKEFPDARLADLIARPNVLVTPHTAFYTTHAVRNMVVKAFDNNLELVEGKEAETPVKV 332
                                    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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J49)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LDHD_LACDA | P26297)
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.

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  1j49
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  1.1.1.28
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LDHD_LACDA | P26297: 1dld 1j4a

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1J49)