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PDBsum entry 1lld

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1lld
Jmol
Contents
Protein chains
313 a.a. *
Ligands
NAD ×2
Waters ×222
* Residue conservation analysis
PDB id:
1lld
Name: Oxidoreductase
Title: Molecular basis of allosteric activation of bacterial l-lact dehydrogenase
Structure: L-lactate dehydrogenase. Chain: a, b. Engineered: yes
Source: Bifidobacterium longum subsp. Longum. Organism_taxid: 1679. Strain: subsp. Longum.
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.179    
Authors: S.Iwata,T.Ohta
Key ref: S.Iwata and T.Ohta (1993). Molecular basis of allosteric activation of bacterial L-lactate dehydrogenase. J Mol Biol, 230, 21-27. PubMed id: 8450537 DOI: 10.1006/jmbi.1993.1122
Date:
08-Jun-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
E8ME30  (LDH2_BIFL2) -  L-lactate dehydrogenase 2
Seq:
Struc:
320 a.a.
313 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.27  - L-lactate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-lactate + NAD+ = pyruvate + NADH
(S)-lactate
+
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly
= pyruvate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1993.1122 J Mol Biol 230:21-27 (1993)
PubMed id: 8450537  
 
 
Molecular basis of allosteric activation of bacterial L-lactate dehydrogenase.
S.Iwata, T.Ohta.
 
  ABSTRACT  
 
The three-dimensional structure of allosteric L-lactate dehydrogenase from Bifidobacterium longum, the first example of a T-state structure of L-lactate dehydrogenase, has been determined to 2.0 A. A comparative study of this structure with the previously reported R-state structure from Bacillus stearothermophilus has revealed the allosteric activation mechanism of the bacterial L-lactate dehydrogenase. The fructose 1,6-bisphosphate-induced conformational change at the effector site and the substrate affinity change at the activity site are clearly shown at a molecular level. Coupling of these changes can be simply explained by a set of concerted rotations between subunits in the tetramer of the enzyme. This T to R transition is the first example for a tetrameric allosteric protein where the rotations occur around each of three axes of symmetry.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18040988 L.A.van den Broek, S.W.Hinz, G.Beldman, J.P.Vincken, and A.G.Voragen (2008).
Bifidobacterium carbohydrases-their role in breakdown and synthesis of (potential) prebiotics.
  Mol Nutr Food Res, 52, 146-163.  
11807949 H.Uchikoba, S.Fushinobu, T.Wakagi, M.Konno, H.Taguchi, and H.Matsuzawa (2002).
Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces.
  Proteins, 46, 206-214.
PDB code: 1ez4
11276087 J.A.Read, V.J.Winter, C.M.Eszes, R.B.Sessions, and R.L.Brady (2001).
Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase.
  Proteins, 43, 175-185.
PDB codes: 1i0z 1i10
9446610 S.Fushinobu, T.Ohta, and H.Matsuzawa (1998).
Homotropic activation via the subunit interaction and allosteric symmetry revealed on analysis of hybrid enzymes of L-lactate dehydrogenase.
  J Biol Chem, 273, 2971-2976.  
9265623 F.J.Bruzzese, and P.R.Connelly (1997).
Allosteric properties of inosine monophosphate dehydrogenase revealed through the thermodynamics of binding of inosine 5'-monophosphate and mycophenolic acid. Temperature dependent heat capacity of binding as a signature of ligand-coupled conformational equilibria.
  Biochemistry, 36, 10428-10438.  
  9212432 K.Savijoki, and A.Palva (1997).
Molecular genetic characterization of the L-lactate dehydrogenase gene (ldhL) of Lactobacillus helveticus and biochemical characterization of the enzyme.
  Appl Environ Microbiol, 63, 2850-2856.  
  8732758 R.Ostendorp, G.Auerbach, and R.Jaenicke (1996).
Extremely thermostable L(+)-lactate dehydrogenase from Thermotoga maritima: cloning, characterization, and crystallization of the recombinant enzyme in its tetrameric and octameric state.
  Protein Sci, 5, 862-873.  
8810336 S.Fushinobu, K.Kamata, S.Iwata, H.Sakai, T.Ohta, and H.Matsuzawa (1996).
Allosteric activation of L-lactate dehydrogenase analyzed by hybrid enzymes with effector-sensitive and -insensitive subunits.
  J Biol Chem, 271, 25611-25616.  
8871566 S.Pietrokovski (1996).
Searching databases of conserved sequence regions by aligning protein multiple-alignments.
  Nucleic Acids Res, 24, 3836-3845.  
  7887607 D.Garmyn, T.Ferain, N.Bernard, P.Hols, and J.Delcour (1995).
Cloning, nucleotide sequence, and transcriptional analysis of the Pediococcus acidilactici L-(+)-lactate dehydrogenase gene.
  Appl Environ Microbiol, 61, 266-272.  
7656036 S.Iwata, K.Kamata, S.Yoshida, T.Minowa, and T.Ohta (1994).
T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control.
  Nat Struct Biol, 1, 176-185.
PDB code: 1lth
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.