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PDBsum entry 1xky

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protein metals Protein-protein interface(s) links
Lyase PDB id
1xky
Jmol
Contents
Protein chains
292 a.a. *
Metals
__K ×10
Waters ×1748
* Residue conservation analysis
PDB id:
1xky
Name: Lyase
Title: Crystal structure of dihydrodipicolinate synthase dapa-2 (ba3935) from bacillus anthracis at 1.94a resolution.
Structure: Dihydrodipicolinate synthase. Chain: a, b, c, d. Engineered: yes
Source: Bacillus anthracis. Organism_taxid: 1392. Gene: dapa-2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.94Å     R-factor:   0.156     R-free:   0.197
Authors: V.Levdikov,E.Blagova,M.J.Fogg,J.A.Brannigan,N.Milioti, A.J.Wilkinson,K.S.Wilson
Key ref:
E.Blagova et al. (2006). Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution. Proteins, 62, 297-301. PubMed id: 16287120 DOI: 10.1002/prot.20684
Date:
30-Sep-04     Release date:   04-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q81WN7  (Q81WN7_BACAN) -  4-hydroxy-tetrahydrodipicolinate synthase
Seq:
Struc:
292 a.a.
292 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.3.3.7  - 4-hydroxy-tetrahydrodipicolinate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5- tetrahydro-(2S)-dipicolinate + H2O
Pyruvate
+ L-aspartate-4-semialdehyde
= (4S)-4-hydroxy-2,3,4,5- tetrahydro-(2S)-dipicolinate
+ H(2)O
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     metabolic process   5 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.20684 Proteins 62:297-301 (2006)
PubMed id: 16287120  
 
 
Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution.
E.Blagova, V.Levdikov, N.Milioti, M.J.Fogg, A.K.Kalliomaa, J.A.Brannigan, K.S.Wilson, A.J.Wilkinson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Aspects of the sequence and structure of dihydrodipicolinate synthase from B. anthracis: (A) Ribbon tracing of the DHDPS subunit colour ramped from the amino- (blue) to the carboxyl-terminus (red). The side chain of the active site lysine 163 is shown in liquorice representation at the centre of the molecule. The view is looking down the axis of the -barrel. (B) Ribbon tracing of the DHDPS tetramer coloured by subunit. (C) Comparison of the active sites of BaDHDPS (blue) and TmDHDPS (green). The two structures were overlayed by least squares methods applied to equivalent C[ ]atoms of their respective A chains. The side chains (shown in stereo) of active site residues for BaDHDPS (TmDHDPS) are shown and labeled. In clockwise orientation from Lys^163 (Lys^161) on the left these are, Tyr^135 (Tyr^132), Arg^140 (Arg^137), Tyr^109 (Tyr^106), Thr^46 (Thr^43), Ser^250 (Asn^251), and Phe^246 (Phe^247). Tyr^109 of BaDHDPS and Tyr^106 from TmDHDPS are colored in cyan and red, respectively, to indicate that these residues are part of the adjacent chain B. In the TmDHDPS, Lys^161 has formed a Schiff base complex with pyruvate. (D) Alignment of the sequences of DHDPS from B. anthracis (Ban), E. coli (Eco), and T. maritima (Tma) with the BaDHDPS secondary structure superposed.
 
  The above figure is reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 62, 297-301) copyright 2006.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20222969 A.Garg, R.Tewari, and G.P.Raghava (2010).
KiDoQ: using docking based energy scores to develop ligand based model for predicting antibacterials.
  BMC Bioinformatics, 11, 125.  
20122228 A.Garg, R.Tewari, and G.P.Raghava (2010).
Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis.
  BMC Bioinformatics, 11, S53.  
19948665 J.E.Voss, S.W.Scally, N.L.Taylor, S.C.Atkinson, M.D.Griffin, C.A.Hutton, M.W.Parker, M.R.Alderton, J.A.Gerrard, R.C.Dobson, C.Dogovski, and M.A.Perugini (2010).
Substrate-mediated stabilization of a tetrameric drug target reveals Achilles heel in anthrax.
  J Biol Chem, 285, 5188-5195.
PDB code: 3hij
  19194017 J.E.Voss, S.W.Scally, N.L.Taylor, C.Dogovski, M.R.Alderton, C.A.Hutton, J.A.Gerrard, M.W.Parker, R.C.Dobson, and M.A.Perugini (2009).
Expression, purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Bacillus anthracis in the presence of pyruvate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 188-191.  
  19255476 S.C.Atkinson, R.C.Dobson, J.M.Newman, M.A.Gorman, C.Dogovski, M.W.Parker, and M.A.Perugini (2009).
Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 253-255.  
  18607102 B.R.Burgess, R.C.Dobson, C.Dogovski, G.B.Jameson, M.W.Parker, and M.A.Perugini (2008).
Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 659-661.  
18787203 R.C.Dobson, M.D.Griffin, S.R.Devenish, F.G.Pearce, C.A.Hutton, J.A.Gerrard, G.B.Jameson, and M.A.Perugini (2008).
Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase.
  Protein Sci, 17, 2080-2090.
PDB code: 3c0j
  18323610 R.C.Dobson, S.C.Atkinson, M.A.Gorman, J.M.Newman, M.W.Parker, and M.A.Perugini (2008).
The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 206-208.  
18361457 S.Manicka, Y.Peleg, T.Unger, S.Albeck, O.Dym, H.M.Greenblatt, G.Bourenkov, V.Lamzin, S.Krishnaswamy, and J.L.Sussman (2008).
Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
  Proteins, 71, 2102-2108.
PDB codes: 2v8z 2v9d
  19052357 S.R.Devenish, J.A.Gerrard, G.B.Jameson, and R.C.Dobson (2008).
The high-resolution structure of dihydrodipicolinate synthase from Escherichia coli bound to its first substrate, pyruvate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1092-1095.  
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.  
17579770 C.A.Hutton, M.A.Perugini, and J.A.Gerrard (2007).
Inhibition of lysine biosynthesis: an evolving antibiotic strategy.
  Mol Biosyst, 3, 458-465.  
  17565178 N.Shimada, B.Mikami, S.Watanabe, and K.Makino (2007).
Preliminary crystallographic analysis of L-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 393-395.  
  17077492 G.Kefala, and M.S.Weiss (2006).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1116-1119.  
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.