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PDBsum entry 1knp

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protein ligands metals links
Oxidoreductase PDB id
1knp
Jmol
Contents
Protein chain
529 a.a. *
Ligands
FAD
SIN
Metals
_NA
Waters ×20
* Residue conservation analysis
PDB id:
1knp
Name: Oxidoreductase
Title: E. Coli l-aspartate oxidase: mutant r386l in complex with succinate
Structure: L-aspartate oxidase. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: nadb. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.233     R-free:   0.281
Authors: R.T.Bossi,A.Mattevi
Key ref:
R.T.Bossi et al. (2002). Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis. Biochemistry, 41, 3018-3024. PubMed id: 11863440 DOI: 10.1021/bi015939r
Date:
19-Dec-01     Release date:   17-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10902  (NADB_ECOLI) -  L-aspartate oxidase
Seq:
Struc:
 
Seq:
Struc:
540 a.a.
529 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.1.4.3.16  - L-aspartate oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + O2 = iminosuccinate + H2O2
L-aspartate
Bound ligand (Het Group name = SIN)
matches with 88.00% similarity
+ O(2)
= iminosuccinate
+ H(2)O(2)
      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!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     L-aspartate:fumarate oxidoreductase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi015939r Biochemistry 41:3018-3024 (2002)
PubMed id: 11863440  
 
 
Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis.
R.T.Bossi, A.Negri, G.Tedeschi, A.Mattevi.
 
  ABSTRACT  
 
L-Aspartate oxidase (Laspo) catalyzes the conversion of L-Asp to iminoaspartate, the first step in the de novo biosynthesis of NAD(+). This bacterial pathway represents a potential drug target since it is absent in mammals. The Laspo R386L mutant was crystallized in the FAD-bound catalytically competent form and its three-dimensional structure determined at 2.5 A resolution in both the native state and in complex with succinate. Comparison of the R386L holoprotein with the wild-type apoenzyme [Mattevi, A., Tedeschi, G., Bacchella, L., Coda, A., Negri, A., and Ronchi, S. (1999) Structure 7, 745-756] reveals that cofactor incorporation leads to the ordering of two polypeptide segments (residues 44-53 and 104-141) and to a 27 degree rotation of the capping domain. This motion results in the formation of the active site cavity, located at the interface between the capping domain and the FAD-binding domain. The structure of the succinate complex indicates that the cavity surface is decorated by two clusters of H-bond donors that anchor the ligand carboxylates. Moreover, Glu121, which is strictly conserved among Laspo sequences, is positioned to interact with the L-Asp alpha-amino group. The architecture of the active site of the Laspo holoenzyme is remarkably similar to that of respiratory fumarate reductases, providing strong evidence for a common mechanism of catalysis in Laspo and flavoproteins of the succinate dehydrogenase/fumarate reductase family. This implies that Laspo is mechanistically distinct from other flavin-dependent amino acid oxidases, such as the prototypical D-amino acid oxidase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20941734 E.A.Bushnell, E.Erdtman, J.Llano, L.A.Eriksson, and J.W.Gauld (2011).
The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase.
  J Comput Chem, 32, 822-834.  
21307570 T.Kurihara (2011).
A mechanistic analysis of enzymatic degradation of organohalogen compounds.
  Biosci Biotechnol Biochem, 75, 189-198.  
18757546 A.Miura, M.Kameya, H.Arai, M.Ishii, and Y.Igarashi (2008).
A soluble NADH-dependent fumarate reductase in the reductive tricarboxylic acid cycle of Hydrogenobacter thermophilus TK-6.
  J Bacteriol, 190, 7170-7177.  
18401503 M.W.van der Kamp, F.Perruccio, and A.J.Mulholland (2008).
High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase.
  Chem Commun (Camb), (), 1874-1876.  
18385138 T.M.Tomasiak, E.Maklashina, G.Cecchini, and T.M.Iverson (2008).
A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II.
  J Biol Chem, 283, 15460-15468.
PDB code: 3cir
17455908 Y.O.You, and W.A.van der Donk (2007).
Mechanistic investigations of the dehydration reaction of lacticin 481 synthetase using site-directed mutagenesis.
  Biochemistry, 46, 5991-6000.  
16430685 J.A.Imlay (2006).
Iron-sulphur clusters and the problem with oxygen.
  Mol Microbiol, 59, 1073-1082.  
15781461 A.Kurata, T.Kurihara, H.Kamachi, and N.Esaki (2005).
2-Haloacrylate reductase, a novel enzyme of the medium chain dehydrogenase/reductase superfamily that catalyzes the reduction of a carbon-carbon double bond of unsaturated organohalogen compounds.
  J Biol Chem, 280, 20286-20291.  
15937336 H.Sakuraba, H.Tsuge, K.Yoneda, N.Katunuma, and T.Ohshima (2005).
Crystal structure of the NAD biosynthetic enzyme quinolinate synthase.
  J Biol Chem, 280, 26645-26648.
PDB code: 1wzu
14527321 G.Cecchini (2003).
Function and structure of complex II of the respiratory chain.
  Annu Rev Biochem, 72, 77.  
14622288 M.H.Hefti, J.Vervoort, and W.J.van Berkel (2003).
Deflavination and reconstitution of flavoproteins.
  Eur J Biochem, 270, 4227-4242.  
12200425 K.R.Messner, and J.A.Imlay (2002).
Mechanism of superoxide and hydrogen peroxide formation by fumarate reductase, succinate dehydrogenase, and aspartate oxidase.
  J Biol Chem, 277, 42563-42571.  
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.