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PDBsum entry 2npx

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Oxidoreductase(h2o2(a)) PDB id
2npx
Jmol
Contents
Protein chain
447 a.a. *
Ligands
FAD
NAD
Waters ×337
* Residue conservation analysis
PDB id:
2npx
Name: Oxidoreductase(h2o2(a))
Title: Nadh binding site and catalysis of nadh peroxidase
Structure: Nadh peroxidase. Chain: a. Engineered: yes
Source: Enterococcus faecalis. Organism_taxid: 1351
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.159    
Authors: T.Stehle,A.Claiborne,G.E.Schulz
Key ref: T.Stehle et al. (1993). NADH binding site and catalysis of NADH peroxidase. Eur J Biochem, 211, 221-226. PubMed id: 8425532
Date:
29-May-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P37062  (NAPE_ENTFA) -  NADH peroxidase
Seq:
Struc:
447 a.a.
447 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.1.11.1.1  - Nadh peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: NADH + H2O2 = NAD+ + 2 H2O
NADH
Bound ligand (Het Group name = NAD)
corresponds exactly
+ H(2)O(2)
= NAD(+)
+ 2 × H(2)O
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  

 

 
    reference    
 
 
Eur J Biochem 211:221-226 (1993)
PubMed id: 8425532  
 
 
NADH binding site and catalysis of NADH peroxidase.
T.Stehle, A.Claiborne, G.E.Schulz.
 
  ABSTRACT  
 
The structure of the complex between cofactor NADH and the enzyme NADH peroxidase from Streptococcus faecalis 10C1 (Enterococcus faecalis) has been determined by crystal soaking, X-ray data collection, model building of NADH and refinement at 0.24-nm resolution based on the known enzyme structure [Stehle, T., Ahmed, S. A., Claiborne, A. & Schulz, G. E. (1991) J. Mol. Biol. 221, 1325-1344]. Apart from NADH, the catalytic center of the enzyme contains FAD and a cysteine that shuttles between thiolate and sulfenic acid states. Unfortunately, this cysteine was irreversibly oxidized to a cysteine sulfonic acid in the established enzyme structure. Based on the geometry of the catalytic center, we discuss the stabilization of the oxidation-sensitive sulfenic acid and propose a reaction mechanism.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18399646 J.R.Wallen, C.Paige, T.C.Mallett, P.A.Karplus, and A.Claiborne (2008).
Pyridine nucleotide complexes with Bacillus anthracis coenzyme A-disulfide reductase: a structural analysis of dual NAD(P)H specificity.
  Biochemistry, 47, 5182-5193.
PDB codes: 3cgb 3cgc 3cgd 3cge
18234830 K.Kubiak, and W.Nowak (2008).
Molecular dynamics simulations of the photoactive protein nitrile hydratase.
  Biophys J, 94, 3824-3838.  
17239398 P.Liu, H.E.Ewis, P.C.Tai, C.D.Lu, and I.T.Weber (2007).
Crystal structure of the Geobacillus stearothermophilus carboxylesterase Est55 and its activation of prodrug CPT-11.
  J Mol Biol, 367, 212-223.
PDB codes: 2ogs 2ogt
16981688 T.C.Mallett, J.R.Wallen, P.A.Karplus, H.Sakai, T.Tsukihara, and A.Claiborne (2006).
Structure of coenzyme A-disulfide reductase from Staphylococcus aureus at 1.54 A resolution.
  Biochemistry, 45, 11278-11289.
PDB code: 1yqz
15328411 E.Malito, A.Alfieri, M.W.Fraaije, and A.Mattevi (2004).
Crystal structure of a Baeyer-Villiger monooxygenase.
  Proc Natl Acad Sci U S A, 101, 13157-13162.
PDB code: 1w4x
15502322 G.T.Lountos, B.R.Riebel, W.B.Wellborn, A.S.Bommarius, and A.M.Orville (2004).
Crystallization and preliminary analysis of a water-forming NADH oxidase from Lactobacillus sanfranciscensis.
  Acta Crystallogr D Biol Crystallogr, 60, 2044-2047.  
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.  
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.  
10956025 E.J.Crane, J.I.Yeh, J.Luba, and A.Claiborne (2000).
Analysis of the kinetic and redox properties of the NADH peroxidase R303M mutant: correlation with the crystal structure.
  Biochemistry, 39, 10353-10364.
PDB code: 1f8w
10679894 P.E.Smith, and J.J.Tanner (2000).
Conformations of nicotinamide adenine dinucleotide (NAD(+)) in various environments.
  J Mol Recognit, 13, 27-34.  
  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
10074352 T.C.Mallett, D.Parsonage, and A.Claiborne (1999).
Equilibrium analyses of the active-site asymmetry in enterococcal NADH oxidase: role of the cysteine-sulfenic acid redox center.
  Biochemistry, 38, 3000-3011.  
9488708 S.B.delCardayre, and J.E.Davies (1998).
Staphylococcus aureus coenzyme A disulfide reductase, a new subfamily of pyridine nucleotide-disulfide oxidoreductase. Sequence, expression, and analysis of cdr.
  J Biol Chem, 273, 5752-5757.  
9738009 S.Vasudevan, T.Tsuruo, and D.R.Rose (1998).
Mode of binding of anti-P-glycoprotein antibody MRK-16 to its antigen. A crystallographic and molecular modeling study.
  J Biol Chem, 273, 25413-25419.
PDB code: 1bln
9628741 T.C.Mallett, and A.Claiborne (1998).
Oxygen reactivity of an NADH oxidase C42S mutant: evidence for a C(4a)-peroxyflavin intermediate and a rate-limiting conformational change.
  Biochemistry, 37, 8790-8802.  
  9336832 C.E.Bell, T.O.Yeates, and D.Eisenberg (1997).
Unusual conformation of nicotinamide adenine dinucleotide (NAD) bound to diphtheria toxin: a comparison with NAD bound to the oxidoreductase enzymes.
  Protein Sci, 6, 2084-2096.  
9214307 E.J.Crane, J.Vervoort, and A.Claiborne (1997).
13C NMR analysis of the cysteine-sulfenic acid redox center of enterococcal NADH peroxidase.
  Biochemistry, 36, 8611-8618.  
8652580 E.J.Crane, D.Parsonage, and A.Claiborne (1996).
The active-site histidine-10 of enterococcal NADH peroxidase is not essential for catalytic activity.
  Biochemistry, 35, 2380-2387.  
8756456 J.I.Yeh, A.Claiborne, and W.G.Hol (1996).
Structure of the native cysteine-sulfenic acid redox center of enterococcal NADH peroxidase refined at 2.8 A resolution.
  Biochemistry, 35, 9951-9957.
PDB code: 1joa
  8976552 R.A.Laskowski, N.M.Luscombe, M.B.Swindells, and J.M.Thornton (1996).
Protein clefts in molecular recognition and function.
  Protein Sci, 5, 2438-2452.  
8805513 T.E.Benson, C.T.Walsh, and J.M.Hogle (1996).
The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls.
  Structure, 4, 47-54.
PDB code: 1mbt
  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 codes are shown on the right.