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PDBsum entry 1dhp

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protein metals links
Synthase PDB id
1dhp
Jmol
Contents
Protein chains
292 a.a. *
Metals
__K ×2
Waters ×344
* Residue conservation analysis
PDB id:
1dhp
Name: Synthase
Title: Dihydrodipicolinate synthase
Structure: Dihydrodipicolinate synthase. Chain: a, b. Synonym: dhdps. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: dapa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.30Å     R-factor:   0.197    
Authors: C.Mirwaldt,I.Korndoerfer,R.Huber
Key ref: C.Mirwaldt et al. (1995). The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution. J Mol Biol, 246, 227-239. PubMed id: 7853400 DOI: 10.1006/jmbi.1994.0078
Date:
09-Feb-95     Release date:   12-Feb-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6L2  (DAPA_ECOLI) -  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   2 terms 
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.1994.0078 J Mol Biol 246:227-239 (1995)
PubMed id: 7853400  
 
 
The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution.
C.Mirwaldt, I.Korndörfer, R.Huber.
 
  ABSTRACT  
 
The crystal structure of dihydrodipicolinate synthase from E. coli was determined by multiple isomorphous replacement methods. The structure was refined at a resolution of 2.5 A and the final R-factor is 19.6% for 32,190 reflections between 10.0 A and 2.5 A and F > 2 sigma (F). The crystallographic asymmetric unit contains two monomers related by approximate 2-fold symmetry. A tetramer with approximate 222 symmetry is built up by crystallographic symmetry. The tetramer is almost planar with no contacts between the subunits related by the non-crystallographic dyad. The active sites are accessible from a wide water-filled channel in the center of the tetramer. The dihydrodipicolinate synthase monomer is composed of two domains. Each polypeptide chain is folded into an 8-fold alpha/beta barrel and a C-terminal alpha-helical domain comprising residues 224 to 292. The fold is similar to that of N-acetylneuraminate lyase. The active site lysine 161 is located in the alpha/beta barrel and has access via two entrances from the C-terminal side of the barrel.
 

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.  
  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.  
18684709 B.R.Burgess, R.C.Dobson, M.F.Bailey, S.C.Atkinson, M.D.Griffin, G.B.Jameson, M.W.Parker, J.A.Gerrard, and M.A.Perugini (2008).
Structure and evolution of a novel dimeric enzyme from a clinically important bacterial pathogen.
  J Biol Chem, 283, 27598-27603.
PDB code: 3daq
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.  
  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.  
16287120 E.Blagova, V.Levdikov, N.Milioti, M.J.Fogg, A.K.Kalliomaa, J.A.Brannigan, K.S.Wilson, and A.J.Wilkinson (2006).
Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution.
  Proteins, 62, 297-301.
PDB codes: 1xky 1xl9
  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.  
15981001 M.A.Perugini, M.D.Griffin, B.J.Smith, L.E.Webb, A.J.Davis, E.Handman, and J.A.Gerrard (2005).
Insight into the self-association of key enzymes from pathogenic species.
  Eur Biophys J, 34, 469-476.  
16041077 R.C.Dobson, M.D.Griffin, G.B.Jameson, and J.A.Gerrard (2005).
The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.
  Acta Crystallogr D Biol Crystallogr, 61, 1116-1124.
PDB codes: 1yxc 1yxd
15265860 A.Theodossis, H.Walden, E.J.Westwick, H.Connaris, H.J.Lamble, D.W.Hough, M.J.Danson, and G.L.Taylor (2004).
The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus.
  J Biol Chem, 279, 43886-43892.
PDB codes: 1w37 1w3i 1w3n 1w3t
12711733 A.C.Joerger, S.Mayer, and A.R.Fersht (2003).
Mimicking natural evolution in vitro: an N-acetylneuraminate lyase mutant with an increased dihydrodipicolinate synthase activity.
  Proc Natl Acad Sci U S A, 100, 5694-5699.
PDB code: 1hl2
11425723 H.Motoyama, H.Yano, Y.Terasaki, and H.Anazawa (2001).
Overproduction of L-Lysine from methanol by Methylobacillus glycogenes derivatives carrying a plasmid with a mutated dapA gene.
  Appl Environ Microbiol, 67, 3064-3070.  
11053844 E.J.Hendry, C.L.Buchanan, R.J.Russell, D.W.Hough, C.D.Reeve, M.J.Danson, and G.L.Taylor (2000).
Preliminary crystallographic studies of an extremely thermostable KDG aldolase from Sulfolobus solfataricus.
  Acta Crystallogr D Biol Crystallogr, 56, 1437-1439.  
9388188 P.C.Babbitt, and J.A.Gerlt (1997).
Understanding enzyme superfamilies. Chemistry As the fundamental determinant in the evolution of new catalytic activities.
  J Biol Chem, 272, 30591-30594.  
8993314 S.Blickling, C.Renner, B.Laber, H.D.Pohlenz, T.A.Holak, and R.Huber (1997).
Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy.
  Biochemistry, 36, 24-33.  
  9165072 S.Blickling, and J.Knäblein (1997).
Feedback inhibition of dihydrodipicolinate synthase enzymes by L-lysine.
  Biol Chem, 378, 207-210.  
9048556 W.E.Karsten (1997).
Dihydrodipicolinate synthase from Escherichia coli: pH dependent changes in the kinetic mechanism and kinetic mechanism of allosteric inhibition by L-lysine.
  Biochemistry, 36, 1730-1739.  
9204286 Y.Lindqvist, and G.Schneider (1997).
Circular permutations of natural protein sequences: structural evidence.
  Curr Opin Struct Biol, 7, 422-427.  
8805555 J.Jia, W.Huang, U.Schörken, H.Sahm, G.A.Sprenger, Y.Lindqvist, and G.Schneider (1996).
Crystal structure of transaldolase B from Escherichia coli suggests a circular permutation of the alpha/beta barrel within the class I aldolase family.
  Structure, 4, 715-724.
PDB code: 1onr
8700867 J.M.Shaver, D.C.Bittel, J.M.Sellner, D.A.Frisch, D.A.Somers, and B.G.Gengenbach (1996).
Single-amino acid substitutions eliminate lysine inhibition of maize dihydrodipicolinate synthase.
  Proc Natl Acad Sci U S A, 93, 1962-1966.  
  8762144 S.Janecek (1996).
Invariant glycines and prolines flanking in loops the strand beta 2 of various (alpha/beta)8-barrel enzymes: a hidden homology?
  Protein Sci, 5, 1136-1143.  
  8844849 T.A.Thanaraj, and P.Argos (1996).
Ribosome-mediated translational pause and protein domain organization.
  Protein Sci, 5, 1594-1612.  
8700866 T.G.Hastings, D.A.Lewis, and M.J.Zigmond (1996).
Role of oxidation in the neurotoxic effects of intrastriatal dopamine injections.
  Proc Natl Acad Sci U S A, 93, 1956-1961.  
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.