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PDBsum entry 1arz

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1arz
Jmol
Contents
Protein chains
270 a.a. *
Ligands
PO4
NAI ×3
PDC ×3
Metals
__K ×2
Waters ×179
* Residue conservation analysis
PDB id:
1arz
Name: Oxidoreductase
Title: Escherichia coli dihydrodipicolinate reductase in complex wi and 2,6 pyridine dicarboxylate
Structure: Dihydrodipicolinate reductase. Chain: a, b, c, d. Synonym: dhpr. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cell_line: bl21. Gene: dapb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.60Å     R-factor:   0.214     R-free:   0.297
Authors: G.Scapin,S.G.Reddy,R.Zheng,J.S.Blanchard
Key ref:
G.Scapin et al. (1997). Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. Biochemistry, 36, 15081-15088. PubMed id: 9398235 DOI: 10.1021/bi9719915
Date:
08-Aug-97     Release date:   14-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P04036  (DAPB_ECOLI) -  4-hydroxy-tetrahydrodipicolinate reductase
Seq:
Struc:
273 a.a.
270 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.17.1.8  - 4-hydroxy-tetrahydrodipicolinate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Bound ligand (Het Group name = PDC)
corresponds exactly
+
NAD(P)(+)
Bound ligand (Het Group name = NAI)
matches with 91.67% similarity
+ H(2)O
= (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate
+ NAD(P)H
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9719915 Biochemistry 36:15081-15088 (1997)
PubMed id: 9398235  
 
 
Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate.
G.Scapin, S.G.Reddy, R.Zheng, J.S.Blanchard.
 
  ABSTRACT  
 
Dihydrodipicolinate reductase catalyzes the NAD(P)H-dependent reduction of the alpha,beta-unsaturated cyclic imine dihydrodipicolinate to form the cyclic imine tetrahydrodipicolinate. The enzyme is a component of the biosynthetic pathway that leads to diaminopimelate and lysine in bacteria and higher plants. Because these pathways are unique to microorganisms and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds. The three-dimensional structure of the ternary complex of Escherichia coli dihydrodipicolinate reductase with NADH and the inhibitor 2,6-pyridinedicarboxylate has been solved using a combination of molecular replacement and noncrystallographic symmetry averaging procedures and refined against 2.6 A resolution data to a crystallographic R-factor of 21.4% (Rfree is 29.7%). The native enzyme is a 120 000 molecular weight tetramer of identical subunits. The refined crystallographic model contains a tetramer, three molecules of NADH, three molecules of inhibitor, one phosphate ion, and 186 water molecules per asymmetric unit. Each subunit consists of two domains connected by two flexible hinge regions. While three of the four subunits of the tetramer have a closed conformation, in which the nicotinamide ring of the cofactor bound to the N-terminal domain and the reducible carbon of the substrate bound to the substrate binding domain are about 3.5 A away, the fourth subunit is unliganded and shows an open conformation, suggesting that the enzyme undergoes a major conformational change upon binding of both substrates. The residues involved in binding of the inhibitor and the residues involved in catalysis have been identified on the basis of the three-dimensional structure. Site-directed mutants have been used to further characterize the role of these residues in binding and catalysis. A chemical mechanism for the enzyme, based on these and previously reported data, is proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20057050 R.Janowski, G.Kefala, and M.S.Weiss (2010).
The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms.
  Acta Crystallogr D Biol Crystallogr, 66, 61-72.
PDB codes: 1yl5 1yl6 1yl7
21581114 L.Hao, C.Mu, and B.Kong (2008).
catena-Poly[[[diacrylato-κO,O'-neodymium(III)]-di-μ-acrylato-κO,O':O';κO:O,O'-[triaqua-neodymium(III)]-di-μ-acrylato-κO,O':O';κO:O,O'] trihydrate].
  Acta Crystallogr Sect E Struct Rep Online, 64, m1492-m1493.  
21201985 S.B.Wang, H.M.He, S.Li, and K.Tang (2008).
Tetra-kis(μ-2,4-difluoro-benzoato)bis-[(2,4-difluoro-benzoato)(1,10-phenanthroline)gadolinium(III)].
  Acta Crystallogr Sect E Struct Rep Online, 64, m516.  
21201598 S.Li, F.L.Zhang, K.Tang, and Y.F.Ma (2008).
Tetra-μ-2,5-difluoro-benzoato-bis-[(2,2'-bipyridine)(2,5-difluoro-benzoato)gadolinium(III)].
  Acta Crystallogr Sect E Struct Rep Online, 64, m1142.  
21202506 S.Li, S.B.Wang, K.Tang, and Y.F.Ma (2008).
Tris[2-(propyl-imino-meth-yl)phenolato-κN,O]cobalt(III).
  Acta Crystallogr Sect E Struct Rep Online, 64, m823.  
21200992 S.Wang, Z.Li, X.Wang, and X.Yu (2008).
Bis(ethano-lato-κO)(5,10,15,20-tetra-phenyl-calix[4]pyrrole)manganese(III) hexa-fluoro-phosphate.
  Acta Crystallogr Sect E Struct Rep Online, 64, m1232.  
18340401 S.Wolterink-van Loo, M.Levisson, M.C.Cabrières, M.C.Franssen, and J.van der Oost (2008).
Characterization of a thermostable dihydrodipicolinate synthase from Thermoanaerobacter tengcongensis.
  Extremophiles, 12, 461-469.  
  21200519 Q.G.Meng, L.T.Wang, Y.Z.Liu, and Y.Pang (2007).
Oxalatobis(propane-1,3-diamine)manganese(II) chloride monohydrate.
  Acta Crystallogr Sect E Struct Rep Online, 64, m170-m171.  
21200552 Q.Meng, L.Wang, Y.Liu, and Y.Pang (2007).
μ-Oxido-bis-{chlorido[tris-(2-pyridylmethyl)amine]manganese(III)} bis-(hexa-fluorido-phosphate).
  Acta Crystallogr Sect E Struct Rep Online, 64, m204.  
18057598 Y.Ma, L.T.Zhang, X.F.Wang, Y.K.He, and Z.B.Han (2007).
A one-dimensional nickel(II) coordination polymer containing 2,6-dipicolinate and dipyrido[3,2-a:2',3'-c]phenazine.
  Acta Crystallogr C, 63, m573-m575.  
  16511139 G.Kefala, R.Janowski, S.Panjikar, C.Mueller-Dieckmann, and M.S.Weiss (2005).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapB (Rv2773c) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 718-721.  
15939021 L.W.Yang, and I.Bahar (2005).
Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes.
  Structure, 13, 893-904.  
15123280 D.S.Sem, B.Bertolaet, B.Baker, E.Chang, A.D.Costache, S.Coutts, Q.Dong, M.Hansen, V.Hong, X.Huang, R.M.Jack, R.Kho, H.Lang, C.T.Ma, D.Meininger, M.Pellecchia, F.Pierre, H.Villar, and L.Yu (2004).
Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox.
  Chem Biol, 11, 185-194.  
12005437 R.A.Norman, M.S.McAlister, J.Murray-Rust, F.Movahedzadeh, N.G.Stoker, and N.Q.McDonald (2002).
Crystal structure of inositol 1-phosphate synthase from Mycobacterium tuberculosis, a key enzyme in phosphatidylinositol synthesis.
  Structure, 10, 393-402.
PDB code: 1gr0
11342032 A.M.Paiva, D.E.Vanderwall, J.S.Blanchard, J.W.Kozarich, J.M.Williamson, and T.M.Kelly (2001).
Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis.
  Biochim Biophys Acta, 1545, 67-77.  
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.