spacer
spacer

PDBsum entry 3tdt

Go to PDB code: 
protein ligands links
Acyltransferase PDB id
3tdt
Jmol
Contents
Protein chain
274 a.a. *
Ligands
COA
26P
Waters ×91
* Residue conservation analysis
PDB id:
3tdt
Name: Acyltransferase
Title: Complex of tetrahydrodipicolinate n-succinyltransferase with 6-oxopimelate and coenzyme a
Structure: Tetrahydrodipicolinate n-succinyltransferase. Chain: a. Synonym: dapd. Engineered: yes
Source: Mycobacterium bovis. Organism_taxid: 1765. Cell_line: bl21. Gene: dapd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.154     R-free:   0.220
Authors: T.W.Beaman,J.S.Blanchard,S.L.Roderick
Key ref:
T.W.Beaman et al. (1998). The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase. Biochemistry, 37, 10363-10369. PubMed id: 9671504 DOI: 10.1021/bi980759b
Date:
06-May-98     Release date:   14-Oct-98    
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
+
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Bound ligand (Het Group name = 26P)
matches with 92.31% similarity
+ H(2)O
=
CoA
Bound ligand (Het Group name = COA)
corresponds exactly
+ 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: 10.1021/bi980759b Biochemistry 37:10363-10369 (1998)
PubMed id: 9671504  
 
 
The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.
T.W.Beaman, J.S.Blanchard, S.L.Roderick.
 
  ABSTRACT  
 
Tetrahydrodipicolinate (THDP) N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to L-2-(succinylamino)-6-oxopimelate and CoA. This reaction represents the committed step of the succinylase branch of the diaminopimelate/L-lysine biosynthetic pathway by which many bacteria synthesize meso-diaminopimelate, a component of peptidoglycan, and L-lysine from L-aspartate. The crystal structures of THDP succinyltransferase in complex with the substrate/cofactor pairs L-2-aminopimelate/coenzyme A and L-2-amino-6-oxopimelate/coenzyme A have been determined and refined to 2.0 A resolution. The active site of the enzyme is a long narrow groove located at the interface between two left-handed parallel beta-helix (LbetaH) structural domains of the trimeric enzyme. On binding the amino acid acceptor and cofactor, this groove is covered by residues from the C-terminus of one subunit and a flexible loop excluded from the LbetaH domain of an adjacent subunit to form a tunnel. This conformational change is directly related to interactions between the enzyme and the bound amino acid substrate and cofactor and serves to shield the ligands from bulk solvent and to orient the nucleophilic amino group of the amino acid acceptor toward the mercaptoethylamine group of the cofactor.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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.  
17698807 A.H.Williams, and C.R.Raetz (2007).
Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase.
  Proc Natl Acad Sci U S A, 104, 13543-13550.
PDB codes: 2qia 2qiv
16835299 A.H.Williams, R.M.Immormino, D.T.Gewirth, and C.R.Raetz (2006).
Structure of UDP-N-acetylglucosamine acyltransferase with a bound antibacterial pentadecapeptide.
  Proc Natl Acad Sci U S A, 103, 10877-10882.
PDB code: 2aq9
16102001 C.Q.Wenzel, C.Daniels, R.A.Keates, D.Brewer, and J.S.Lam (2005).
Evidence that WbpD is an N-acetyltransferase belonging to the hexapeptide acyltransferase superfamily and an important protein for O-antigen biosynthesis in Pseudomonas aeruginosa PAO1.
  Mol Microbiol, 57, 1288-1303.  
15975504 J.Micklefield (2005).
Nature's protection racket.
  Chem Biol, 12, 611-613.  
15333931 J.Gorman, and L.Shapiro (2004).
Structure of serine acetyltransferase from Haemophilus influenzae Rd.
  Acta Crystallogr D Biol Crystallogr, 60, 1600-1605.
PDB code: 1s80
15211513 L.L.Videau, W.B.Arendall, and J.S.Richardson (2004).
The cis-Pro touch-turn: a rare motif preferred at functional sites.
  Proteins, 56, 298-309.  
15231846 V.E.Pye, A.P.Tingey, R.L.Robson, and P.C.Moody (2004).
The structure and mechanism of serine acetyltransferase from Escherichia coli.
  J Biol Chem, 279, 40729-40736.
PDB code: 1t3d
12771141 L.E.Kehoe, J.Snidwongse, P.Courvalin, J.B.Rafferty, and I.A.Murray (2003).
Structural basis of Synercid (quinupristin-dalfopristin) resistance in Gram-positive bacterial pathogens.
  J Biol Chem, 278, 29963-29970.
PDB codes: 1mr7 1mr9 1mrl
11910040 T.W.Beaman, K.W.Vogel, D.G.Drueckhammer, J.S.Blanchard, and S.L.Roderick (2002).
Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase.
  Protein Sci, 11, 974-979.
PDB codes: 1kgq 1kgt
11329257 L.R.Olsen, and S.L.Roderick (2001).
Structure of the Escherichia coli GlmU pyrophosphorylase and acetyltransferase active sites.
  Biochemistry, 40, 1913-1921.
PDB code: 1hv9
10480918 T.J.Wyckoff, and C.R.Raetz (1999).
The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase. Chemical modification and site-directed mutagenesis.
  J Biol Chem, 274, 27047-27055.  
10508663 T.L.Born, and J.S.Blanchard (1999).
Structure/function studies on enzymes in the diaminopimelate pathway of bacterial cell wall biosynthesis.
  Curr Opin Chem Biol, 3, 607-613.  
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.