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PDBsum entry 1ges

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Oxidoreductase(flavoenzyme) PDB id
1ges
Jmol
Contents
Protein chains
448 a.a. *
Ligands
FAD ×2
Waters ×585
* Residue conservation analysis
PDB id:
1ges
Name: Oxidoreductase(flavoenzyme)
Title: Anatomy of an engineered NAD-binding site
Structure: Glutathione reductase. Chain: a, b. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.74Å     R-factor:   0.168    
Authors: P.R.E.Mittl,G.E.Schulz
Key ref: P.R.Mittl et al. (1994). Anatomy of an engineered NAD-binding site. Protein Sci, 3, 1504-1514. PubMed id: 7833810 DOI: 10.1002/pro.5560030916
Date:
18-Jan-94     Release date:   01-Nov-94    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06715  (GSHR_ECOLI) -  Glutathione reductase
Seq:
Struc:
450 a.a.
448 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
DOI no: 10.1002/pro.5560030916 Protein Sci 3:1504-1514 (1994)
PubMed id: 7833810  
 
 
Anatomy of an engineered NAD-binding site.
P.R.Mittl, A.Berry, N.S.Scrutton, R.N.Perham, G.E.Schulz.
 
  ABSTRACT  
 
The coenzyme specificity of Escherichia coli glutathione reductase was switched from NADP to NAD by modifying the environment of the 2'-phosphate binding site through a set of point mutations: A179G, A183G, V197E, R198M, K199F, H200D, and R204P (Scrutton NS, Berry A, Perham RN, 1990, Nature 343:38-43). In order to analyze the structural changes involved, we have determined 4 high-resolution crystal structures, i.e., the structures of the wild-type enzyme (1.86 A resolution, R-factor of 16.8%), of the wild-type enzyme ligated with NADP (2.0 A, 20.8%), of the NAD-dependent mutant (1.74 A, 16.8%), and of the NAD-dependent mutant ligated with NAD (2.2 A, 16.9%). A comparison of these structures reveals subtle differences that explain details of the specificity change. In particular, a peptide rotation occurs close to the adenosine ribose, with a concomitant change of the ribose pucker. The mutations cause a contraction of the local chain fold. Furthermore, the engineered NAD-binding site assumes a less rigid structure than the NADP site of the wild-type enzyme. A superposition of the ligated structures shows a displacement of NAD versus NADP such that the electron pathway from the nicotinamide ring to FAD is elongated, which may explain the lower catalytic efficiency of the mutant. Because the nicotinamide is as much as 15 A from the sites of the mutations, this observation reminds us that mutations may have important long-range consequences that are difficult to anticipate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19201968 R.Zhang, Y.Xu, Y.Sun, W.Zhang, and R.Xiao (2009).
Ser67Asp and His68Asp substitutions in candida parapsilosis carbonyl reductase alter the coenzyme specificity and enantioselectivity of ketone reduction.
  Appl Environ Microbiol, 75, 2176-2183.  
19668867 X.Liu, and S.J.Sturla (2009).
Profiling patterns of glutathione reductase inhibition by the natural product illudin S and its acylfulvene analogues.
  Mol Biosyst, 5, 1013-1024.  
18566346 R.Zhang, G.Zhu, W.Zhang, S.Cao, X.Ou, X.Li, M.Bartlam, Y.Xu, X.C.Zhang, and Z.Rao (2008).
Crystal structure of a carbonyl reductase from Candida parapsilosis with anti-Prelog stereospecificity.
  Protein Sci, 17, 1412-1423.
PDB code: 3ctm
17181540 J.B.Vicente, F.M.Scandurra, J.V.Rodrigues, M.Brunori, P.Sarti, M.Teixeira, and A.Giuffrè (2007).
Kinetics of electron transfer from NADH to the Escherichia coli nitric oxide reductase flavorubredoxin.
  FEBS J, 274, 677-686.  
15454452 P.A.van den Berg, A.van Hoek, and A.J.Visser (2004).
Evidence for a novel mechanism of time-resolved flavin fluorescence depolarization in glutathione reductase.
  Biophys J, 87, 2577-2586.  
15099733 R.Aroul-Selvam, T.Hubbard, and R.Sasidharan (2004).
Domain insertions in protein structures.
  J Mol Biol, 338, 633-641.  
11854240 A.Purkayastha, L.A.McCue, and K.A.McDonough (2002).
Identification of a Mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions.
  Infect Immun, 70, 1518-1529.  
11329263 A.Gutierrez, L.Y.Lian, C.R.Wolf, N.S.Scrutton, and G.C.Roberts (2001).
Stopped-flow kinetic studies of flavin reduction in human cytochrome P450 reductase and its component domains.
  Biochemistry, 40, 1964-1975.  
10998235 G.A.Ziegler, and G.E.Schulz (2000).
Crystal structures of adrenodoxin reductase in complex with NADP+ and NADPH suggesting a mechanism for the electron transfer of an enzyme family.
  Biochemistry, 39, 10986-10995.
PDB codes: 1e1k 1e1l 1e1m 1e1n
11054119 N.E.Labrou, D.J.Rigden, and Y.D.Clonis (2000).
Characterization of the NAD+ binding site of Candida boidinii formate dehydrogenase by affinity labelling and site-directed mutagenesis.
  Eur J Biochem, 267, 6657-6664.  
  10548046 J.J.Barycki, L.K.O'Brien, J.J.Birktoft, A.W.Strauss, and L.J.Banaszak (1999).
Pig heart short chain L-3-hydroxyacyl-CoA dehydrogenase revisited: sequence analysis and crystal structure determination.
  Protein Sci, 8, 2010-2018.
PDB code: 3hdh
  10493573 J.J.Tanner, S.C.Tu, L.J.Barbour, C.L.Barnes, and K.L.Krause (1999).
Unusual folded conformation of nicotinamide adenine dinucleotide bound to flavin reductase P.
  Protein Sci, 8, 1725-1732.
PDB code: 2bkj
10368293 M.Singleton, M.Isupov, and J.Littlechild (1999).
X-ray structure of pyrrolidone carboxyl peptidase from the hyperthermophilic archaeon Thermococcus litoralis.
  Structure, 7, 237-244.
PDB code: 1a2z
10591107 S.S.Brody, S.P.Gough, and C.G.Kannangara (1999).
Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins.
  Proteins, 37, 485-493.
PDB codes: 1b29 1b61
  8771196 Y.Zhang, C.S.Bond, S.Bailey, M.L.Cunningham, A.H.Fairlamb, and W.N.Hunter (1996).
The crystal structure of trypanothione reductase from the human pathogen Trypanosoma cruzi at 2.3 A resolution.
  Protein Sci, 5, 52-61.
PDB code: 1aog
  7833810 P.R.Mittl, A.Berry, N.S.Scrutton, R.N.Perham, and G.E.Schulz (1994).
Anatomy of an engineered NAD-binding site.
  Protein Sci, 3, 1504-1514.
PDB codes: 1ges 1get 1geu
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.