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PDBsum entry 1ez4

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ez4
Jmol
Contents
Protein chains
307 a.a. *
Ligands
NAD ×4
Waters ×785
* Residue conservation analysis
PDB id:
1ez4
Name: Oxidoreductase
Title: Crystal structure of non-allosteric l-lactate dehydrogenase from lactobacillus pentosus at 2.3 angstrom resolution
Structure: Lactate dehydrogenase. Chain: a, b, c, d. Engineered: yes
Source: Lactobacillus pentosus. Organism_taxid: 1589. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.205     R-free:   0.241
Authors: H.Uchikoba,S.Fushinobu,T.Wakagi,M.Konno,H.Taguchi, H.Matsuzawa
Key ref:
H.Uchikoba et al. (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. PubMed id: 11807949 DOI: 10.1002/prot.1165
Date:
10-May-00     Release date:   28-Dec-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56511  (LDH_LACPE) -  L-lactate dehydrogenase
Seq:
Struc:
320 a.a.
307 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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: 10.1002/prot.1165 Proteins 46:206-214 (2002)
PubMed id: 11807949  
 
 
Crystal structure of non-allosteric L-lactate dehydrogenase from Lactobacillus pentosus at 2.3 A resolution: specific interactions at subunit interfaces.
H.Uchikoba, S.Fushinobu, T.Wakagi, M.Konno, H.Taguchi, H.Matsuzawa.
 
  ABSTRACT  
 
L-Lactate dehydrogenase (LDH) from Lactobacillus pentosus is a non-allosteric enzyme, which shows, however, high sequence similarity to allosteric LDHs from certain bacteria. To elucidate the structural basis of the absence of allostery of L. pentosus LDH (LPLDH), we determined the crystal structure of LPLDH at 2.3 A resolution. Bacterial LDHs are tetrameric enzymes composed of identical subunits and exhibit 222 symmetry. The quaternary structure of LPLDH was similar to the active conformation of allosteric LDHs. Structural analysis revealed that the subunit interfaces of LPLDH are optimized mainly through hydrophilic interactions rather than hydrophobic interactions, compared with other LDHs. The subunit interfaces of LPLDH are more specifically stabilized by increased numbers of intersubunit salt bridges and hydrogen bonds, and higher geometrical complementarity. Such high specificity at the subunit interfaces should hinder the rearrangement of the quaternary structure needed for allosteric regulation and thus explain the "non-allostery" of LPLDH.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (2F[o]-F[c]) electron density map of LPLDH. a: The RT structure in the vicinity of the active site. The map was contoured at 1 . b: The 100K structure. The map was contoured at 1.5 . Figure 2 was made with the O graphics program.
Figure 4.
Figure 4. Intersubunit interactions of LPLDH. (a) Hydrogen bonds in the N-terminal region at the R-axis interface. Ribbon models of B and C subunits are shown in different colors (blue and green). The R axis is normal as to the plane of this picture. The side chains of residues Asn19, His20, Gln21, and Asp264, and the main chain carbonyl groups of Gly295 involved in intersubunit hydrogen bonds are shown as a ball and stick model. Hydrogen bonds are shown by broken lines. (b) Intersubunit salt bridge network formed at the Q-axis interface. Ribbon models of A and B subunits are shown in different colors (red and blue). The side chains of residues involved in the intersubunit salt-bridge network are shown as a ball and stick model. Salt bridges are shown by broken lines. Figure 4 was made with the programs MOLSCRIPT and Raster3D.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2002, 46, 206-214) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17944947 P.Gaspar, A.R.Neves, C.A.Shearman, M.J.Gasson, A.M.Baptista, D.L.Turner, C.M.Soares, and H.Santos (2007).
The lactate dehydrogenases encoded by the ldh and ldhB genes in Lactococcus lactis exhibit distinct regulation and catalytic properties - comparative modeling to probe the molecular basis.
  FEBS J, 274, 5924-5936.  
15382234 K.Gunasekaran, B.Ma, and R.Nussinov (2004).
Is allostery an intrinsic property of all dynamic proteins?
  Proteins, 57, 433-443.  
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.