Linked Life Data

12054772

Source:http://linkedlifedata.com/resource/pubmed/id/12054772

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2002-6-10
pubmed:databankReference
pubmed:abstractText
NAD-dependent Lactobacillus bulgaricus D-Lactate dehydrogenase (D-LDHb) catalyses the reversible conversion of pyruvate into D-lactate. Crystals of D-LDHb complexed with NADH were grown and X-ray data collected to 2.2 A. The structure of D-LDHb was solved by molecular replacement using the dimeric Lactobacillus helveticus D-LDH as a model and was refined to an R-factor of 20.7%. The two subunits of the enzyme display strong asymmetry due to different crystal environments. The opening angles of the two catalytic domains with respect to the core coenzyme binding domains differ by 16 degrees. Subunit A is in an "open" conformation typical for a dehydrogenase apo enzyme and subunit B is "closed". The NADH-binding site in subunit A is only 30% occupied, while in subunit B it is fully occupied and there is a sulphate ion in the substrate-binding pocket. A pyruvate molecule has been modelled in the active site and its orientation is in agreement with existing kinetic and structural data. On domain closure, a cluster of hydrophobic residues packs tightly around the methyl group of the modelled pyruvate molecule. At least three residues from this cluster govern the substrate specificity. Substrate binding itself contributes to the stabilisation of domain closure and activation of the enzyme. In pyruvate reduction, D-LDH can adapt another protonated residue, a lysine residue, to accomplish the role of the acid catalyst His296. Required lowering of the lysine pK(a) value is explained on the basis of the H296K mutant structure.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
0022-2836
pubmed:author
pubmed:copyrightInfo
Copyright 2002 Elsevier Science Ltd.
pubmed:issnType
Print
pubmed:day
19
pubmed:volume
318
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
109-19
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed-meshheading:12054772-Binding Sites, pubmed-meshheading:12054772-Catalysis, pubmed-meshheading:12054772-Dimerization, pubmed-meshheading:12054772-Enzyme Activation, pubmed-meshheading:12054772-Escherichia coli, pubmed-meshheading:12054772-Kinetics, pubmed-meshheading:12054772-L-Lactate Dehydrogenase, pubmed-meshheading:12054772-Lactate Dehydrogenases, pubmed-meshheading:12054772-Lactobacillus, pubmed-meshheading:12054772-Lysine, pubmed-meshheading:12054772-Models, Molecular, pubmed-meshheading:12054772-Mutation, pubmed-meshheading:12054772-NAD, pubmed-meshheading:12054772-Protein Conformation, pubmed-meshheading:12054772-Protons, pubmed-meshheading:12054772-Pyruvates, pubmed-meshheading:12054772-Recombinant Proteins, pubmed-meshheading:12054772-Rotation, pubmed-meshheading:12054772-Sensitivity and Specificity, pubmed-meshheading:12054772-Solutions, pubmed-meshheading:12054772-Substrate Specificity, pubmed-meshheading:12054772-Sulfates
pubmed:year
2002
pubmed:articleTitle
Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus.
pubmed:affiliation
European Molecular Biology Laboratory Hamburg Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany. arazeto@gwdg.de
pubmed:publicationType
Journal Article, Comparative Study