PDBsum entry 1ie3

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
312 a.a. *
NAD ×4
Waters ×166
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of r153c e. Coli malate dehydrogenase
Structure: Malate dehydrogenase. Chain: a, b, c, d. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: mdh. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.50Å     R-factor:   0.186     R-free:   0.252
Authors: J.K.Bell,H.P.Yennawar,S.K.Wright,J.R.Thompson,R.E.Viola, L.J.Banaszak
Key ref:
J.K.Bell et al. (2001). Structural analyses of a malate dehydrogenase with a variable active site. J Biol Chem, 276, 31156-31162. PubMed id: 11389141 DOI: 10.1074/jbc.M100902200
05-Apr-01     Release date:   19-Sep-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P61889  (MDH_ECOLI) -  Malate dehydrogenase
312 a.a.
312 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Malate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Citric acid cycle
      Reaction: (S)-malate + NAD+ = oxaloacetate + NADH
Bound ligand (Het Group name = PYR)
matches with 66.00% similarity
Bound ligand (Het Group name = NAD)
corresponds exactly
= oxaloacetate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     oxidation-reduction process   8 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1074/jbc.M100902200 J Biol Chem 276:31156-31162 (2001)
PubMed id: 11389141  
Structural analyses of a malate dehydrogenase with a variable active site.
J.K.Bell, H.P.Yennawar, S.K.Wright, J.R.Thompson, R.E.Viola, L.J.Banaszak.
Malate dehydrogenase specifically oxidizes malate to oxaloacetate. The specificity arises from three arginines in the active site pocket that coordinate the carboxyl groups of the substrate and stabilize the newly forming hydroxyl/keto group during catalysis. Here, the role of Arg-153 in distinguishing substrate specificity is examined by the mutant R153C. The x-ray structure of the NAD binary complex at 2.1 A reveals two sulfate ions bound in the closed form of the active site. The sulfate that occupies the substrate binding site has been translated approximately 2 A toward the opening of the active site cavity. Its new location suggests that the low catalytic turnover observed in the R153C mutant may be due to misalignment of the hydroxyl or ketone group of the substrate with the appropriate catalytic residues. In the NAD.pyruvate ternary complex, the monocarboxylic inhibitor is bound in the open conformation of the active site. The pyruvate is coordinated not by the active site arginines, but through weak hydrogen bonds to the amide backbone. Energy minimized molecular models of unnatural analogues of R153C (Wright, S. K., and Viola, R. E. (2001) J. Biol. Chem. 276, 31151-31155) reveal that the regenerated amino and amido side chains can form favorable hydrogen-bonding interactions with the substrate, although a return to native enzymatic activity is not observed. The low activity of the modified R153C enzymes suggests that precise positioning of the guanidino side chain is essential for optimal orientation of the substrate.
  Selected figure(s)  
Figure 3.
Fig. 3. Comparison of sulfate positions in R153C eMDH and cytMDH. A C trace of the active site loop from R153C eMDH·NAD·pyruvate (gray), R153C eMDH·NAD (white), and cytMDH·NAD (dark gray) (20). The three structures were superimposed using the LSQ options within O (11). The sulfate ion, labeled C, of cytMDH when compared with sulfate A of the R153C·NAD structure is translated ~2 Å farther into the active site. The hydrogen bonds between the sulfate and Ser-225 and Arg-153 provide the impetus for this translation.
Figure 5.
Fig. 5. Models of the chemical modifications at R153C eMDH. A, the active site of native eMDH shows the theoretical position of the malate with respect to the three coordinating arginines, Arg-81, Arg-87, and Arg-153. The potential hydrogen bonding interactions of the chemically modified cysteine at position 153, EAm and PAm (B), PAd and AAd (C), AAn (D), and Ac (E), are depicted by black lines drawn between acceptor and donor. An alternate rotamer is depicted for Ac, labeled Ac', that has the side chain interacting with solvent.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 31156-31162) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19724119 J.Zaitseva, K.M.Meneely, and A.L.Lamb (2009).
Structure of Escherichia coli malate dehydrogenase at 1.45 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 866-869.
PDB code: 3hhp
17264923 P.Blondeau, M.Segura, R.Pérez-Fernández, and Mendoza (2007).
Molecular recognition of oxoanions based on guanidinium receptors.
  Chem Soc Rev, 36, 198-210.  
15670147 B.Cox, M.M.Chit, T.Weaver, C.Gietl, J.Bailey, E.Bell, and L.Banaszak (2005).
Organelle and translocatable forms of glyoxysomal malate dehydrogenase. The effect of the N-terminal presequence.
  FEBS J, 272, 643-654.
PDB codes: 1sev 1smk
15317584 A.K.Tripathi, P.V.Desai, A.Pradhan, S.I.Khan, M.A.Avery, L.A.Walker, and B.L.Tekwani (2004).
An alpha-proteobacterial type malate dehydrogenase may complement LDH function in Plasmodium falciparum. Cloning and biochemical characterization of the enzyme.
  Eur J Biochem, 271, 3488-3502.  
15048835 R.Das, and M.Gerstein (2004).
A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens.
  Proteins, 55, 455-463.  
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.