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PDBsum entry 1kgt

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Transferase PDB id
1kgt
Jmol
Contents
Protein chain
274 a.a. *
Ligands
PML
SCA
Waters ×58
* Residue conservation analysis
PDB id:
1kgt
Name: Transferase
Title: Crystal structure of tetrahydrodipicolinate n-succinyltransf complex with pimelate and succinyl-coa
Structure: 2,3,4,5-tetrahydropyridine-2-carboxylate n- succinyltransferase. Chain: a. Synonym: tetrahydrodipicolinate n-succinyltransferase, thp succinyltransferase, tetrahydropicolinate succinylase. Engineered: yes
Source: Mycobacterium bovis. Organism_taxid: 1765. Gene: dapd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.171     R-free:   0.261
Authors: T.W.Beaman,K.W.Vogel,D.G.Drueckhammer,J.S.Blanchard,S.L.Rode
Key ref:
T.W.Beaman et al. (2002). Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase. Protein Sci, 11, 974-979. PubMed id: 11910040 DOI: 10.1110/ps.4310102
Date:
28-Nov-01     Release date:   03-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56220  (DAPD_UNKP) -  2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Seq:
Struc:
274 a.a.
274 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.117  - 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Lysine biosynthesis (later stages)
      Reaction: Succinyl-CoA + (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + H2O = CoA + N-succinyl-L-2-amino-6-oxoheptanedioate
Succinyl-CoA
Bound ligand (Het Group name = SCA)
corresponds exactly
+
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Bound ligand (Het Group name = PML)
matches with 91.67% similarity
+ H(2)O
= CoA
+ N-succinyl-L-2-amino-6-oxoheptanedioate
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     cellular amino acid biosynthetic process   4 terms 
  Biochemical function     transferase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.4310102 Protein Sci 11:974-979 (2002)
PubMed id: 11910040  
 
 
Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase.
T.W.Beaman, K.W.Vogel, D.G.Drueckhammer, J.S.Blanchard, S.L.Roderick.
 
  ABSTRACT  
 
Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. We have solved the X-ray crystal structures of DapD in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog, succinamide-CoA. These structures define the binding conformation of the cofactor succinyl group and its interactions with the enzyme and place its thioester carbonyl carbon in close proximity to the nucleophilic 2-amino group of the acceptor, in support of a direct attack ternary complex mechanism. The acyl group specificity differences between homologous tetrahydrodipicolinate N-acetyl- and N-succinyltransferases can be rationalized with reference to at least three amino acids that interact with or give accessible active site volume to the cofactor succinyl group. These residues account at least in part for the substrate specificity that commits metabolic intermediates to either the succinylase or acetylase branches of the meso-diaminopimelate/lysine biosynthetic pathway.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) The reaction sequence leading from tetrahydrodipicolinate to lysine via the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway. (B) The substrates and analogs used in this study.
 
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2002, 11, 974-979) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  19098440 K.C.Kunes, S.C.Clark, D.L.Cox, and R.R.Singh (2008).
Left handed beta helix models for mammalian prion fibrils.
  Prion, 2, 81-90.  
  18765924 L.Schuldt, S.Weyand, G.Kefala, and M.S.Weiss (2008).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of tetrahydrodipicolinate-N-succinyltransferase (Rv1201c) from Mycobacterium tuberculosis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 863-866.  
17507985 P.F.Widboom, E.N.Fielding, Y.Liu, and S.D.Bruner (2007).
Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis.
  Nature, 447, 342-345.
PDB code: 2np9
17335097 Y.Liu, and S.D.Bruner (2007).
Rational manipulation of carrier-domain geometry in nonribosomal peptide synthetases.
  Chembiochem, 8, 617-621.  
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.