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PDBsum entry 1tdt

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protein Protein-protein interface(s) links
Transferase PDB id
1tdt
Jmol PyMol
Contents
Protein chains
256 a.a. *
Waters ×215
* Residue conservation analysis
PDB id:
1tdt
Name: Transferase
Title: Three-dimensional structure of tetrahydrodipicolinate-n- succinlytransferase
Structure: Tetrahydrodipicolinate-n-succinlytransferase. Chain: a, b, c. Synonym: thdp-succinyltransferase, dapd. Engineered: yes
Source: Mycobacterium bovis. Organism_taxid: 1765. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.170     R-free:   0.230
Authors: T.W.Beaman,D.W.Binder,J.S.Blanchard,S.L.Roderick
Key ref:
T.W.Beaman et al. (1997). Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase. Biochemistry, 36, 489-494. PubMed id: 9012664 DOI: 10.1021/bi962522q
Date:
19-Nov-96     Release date:   05-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P56220  (DAPD_UNKP) -  2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Seq:
Struc:
274 a.a.
256 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
+ 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: 10.1021/bi962522q Biochemistry 36:489-494 (1997)
PubMed id: 9012664  
 
 
Three-dimensional structure of tetrahydrodipicolinate N-succinyltransferase.
T.W.Beaman, D.A.Binder, J.S.Blanchard, S.L.Roderick.
 
  ABSTRACT  
 
The conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA is catalyzed by tetrahydrodipicolinate N-succinyltransferase and is the committed step in the succinylase pathway by which bacteria synthesize L-lysine and meso-diaminopimelate, a component of peptidoglycan. The X-ray crystal structure of THDP succinyltransferase has been determined to 2.2 A resolution and has been refined to a crystallographic R-factor of 17.0%. The enzyme is trimeric and displays the left-handed parallel beta-helix (L beta H) structural motif encoded by the "hexapeptide repeat" amino acid sequence motif [Raetz, C.R.H., & Roderick, S.L. (1995) Science 270, 997-1000]. The approximate location of the active site of THDP succinyltransferase is suggested by the proximity of binding sites for two inhibitors: p-(chloromercuri)benzenesulfonic acid and cobalt ion, both of which bind to the L beta H domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20564049 A.Das, and C.Mukhopadhyay (2010).
LpxA: a natural nanotube.
  Biopolymers, 93, 845-853.  
20400541 Z.Zhang, J.Akutsu, and Y.Kawarabayasi (2010).
Identification of novel acetyltransferase activity on the thermostable protein ST0452 from Sulfolobus tokodaii strain 7.
  J Bacteriol, 192, 3287-3293.  
19655786 C.M.Bartling, and C.R.Raetz (2009).
Crystal structure and acyl chain selectivity of Escherichia coli LpxD, the N-acyltransferase of lipid A biosynthesis.
  Biochemistry, 48, 8672-8683.
PDB code: 3eh0
19525232 H.J.Lee, B.Rakić, M.Gilbert, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2009).
Structural and kinetic characterizations of the polysialic acid O-acetyltransferase OatWY from Neisseria meningitidis.
  J Biol Chem, 284, 24501-24511.
PDB codes: 2wlc 2wld 2wle 2wlf 2wlg
19448740 M.Demendi, and C.Creuzenet (2009).
Cj1123c (PglD), a multifaceted acetyltransferase from Campylobacter jejuni.
  Biochem Cell Biol, 87, 469-483.  
  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.  
18667421 N.B.Olivier, and B.Imperiali (2008).
Crystal Structure and Catalytic Mechanism of PglD from Campylobacter jejuni.
  J Biol Chem, 283, 27937-27946.
PDB codes: 3bss 3bsw 3bsy
17519228 A.K.Bergfeld, H.Claus, U.Vogel, and M.Mühlenhoff (2007).
Biochemical characterization of the polysialic acid-specific O-acetyltransferase NeuO of Escherichia coli K1.
  J Biol Chem, 282, 22217-22227.  
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.  
15920617 M.A.Hefford, S.D'Aoust, T.D.Cyr, J.W.Austin, G.Sanders, E.Kheradpir, and M.L.Kalmokoff (2005).
Proteomic and microscopic analysis of biofilms formed by Listeria monocytogenes 568.
  Can J Microbiol, 51, 197-208.  
15692569 X.Jin, M.A.Ballicora, J.Preiss, and J.H.Geiger (2005).
Crystal structure of potato tuber ADP-glucose pyrophosphorylase.
  EMBO J, 24, 694-704.
PDB codes: 1yp2 1yp3 1yp4
15044493 C.R.Sweet, A.H.Williams, M.J.Karbarz, C.Werts, S.R.Kalb, R.J.Cotter, and C.R.Raetz (2004).
Enzymatic synthesis of lipid A molecules with four amide-linked acyl chains. LpxA acyltransferases selective for an analog of UDP-N-acetylglucosamine in which an amine replaces the 3"-hydroxyl group.
  J Biol Chem, 279, 25411-25419.  
15390264 W.Qiu, R.Shi, M.L.Lu, M.Zhou, P.H.Roy, J.Lapointe, and S.X.Lin (2004).
Crystal structure of chloramphenicol acetyltransferase B2 encoded by the multiresistance transposon Tn2424.
  Proteins, 57, 858-861.  
12045108 C.R.Raetz, and C.Whitfield (2002).
Lipopolysaccharide endotoxins.
  Annu Rev Biochem, 71, 635-700.  
12015145 E.K.Leinala, P.L.Davies, and Z.Jia (2002).
Crystal structure of beta-helical antifreeze protein points to a general ice binding model.
  Structure, 10, 619-627.
PDB code: 1l0s
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
11937062 X.G.Wang, L.R.Olsen, and S.L.Roderick (2002).
Structure of the lac operon galactoside acetyltransferase.
  Structure, 10, 581-588.
PDB codes: 1kqa 1krr 1kru 1krv
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.  
11717516 L.Lo Leggio, F.Dal Degan, P.Poulsen, S.O.Sørensen, K.Harlow, P.Harris, and S.Larsen (2001).
Crystallization and preliminary X-ray analysis of maltose O-acetyltransferase.
  Acta Crystallogr D Biol Crystallogr, 57, 1915-1918.  
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
11173485 L.R.Olsen, Y.Tian, and S.L.Roderick (2001).
Purification, crystallization and preliminary X-ray data for Escherichia coli GlmU: a bifunctional acetyltransferase/uridyltransferase.
  Acta Crystallogr D Biol Crystallogr, 57, 296-297.  
11168407 M.Wirtz, O.Berkowitz, M.Droux, and R.Hell (2001).
The cysteine synthase complex from plants. Mitochondrial serine acetyltransferase from Arabidopsis thaliana carries a bifunctional domain for catalysis and protein-protein interaction.
  Eur J Biochem, 268, 686-693.  
10737931 B.Schuler, F.Fürst, F.Osterroth, S.Steinbacher, R.Huber, and R.Seckler (2000).
Plasticity and steric strain in a parallel beta-helix: rational mutations in the P22 tailspike protein.
  Proteins, 39, 89.
PDB codes: 1qq1 1qrb 1qrc
11123920 D.E.Kamen, Y.Griko, and R.W.Woody (2000).
The stability, structural organization, and denaturation of pectate lyase C, a parallel beta-helix protein.
  Biochemistry, 39, 15932-15943.  
  11206055 J.F.Kreisberg, S.D.Betts, and J.King (2000).
Beta-helix core packing within the triple-stranded oligomerization domain of the P22 tailspike.
  Protein Sci, 9, 2338-2343.  
10978542 K.S.Smith, and J.G.Ferry (2000).
Prokaryotic carbonic anhydrases.
  FEMS Microbiol Rev, 24, 335-366.  
10771435 M.Sugantino, and S.L.Roderick (2000).
Expression, purification and crystallization of enterococcus faecium streptogramin A acetyltransferase.
  Acta Crystallogr D Biol Crystallogr, 56, 640-642.  
10428949 K.Brown, F.Pompeo, S.Dixon, D.Mengin-Lecreulx, C.Cambillau, and Y.Bourne (1999).
Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily.
  EMBO J, 18, 4096-4107.
PDB codes: 1fwy 1fxj
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.  
10531507 X.G.Wang, and S.L.Roderick (1999).
Expression, purification, crystallization and preliminary x-ray data of Escherichia coli galactoside acetyltransferase.
  Acta Crystallogr D Biol Crystallogr, 55, 1955-1957.  
  9620966 A.Wehrmann, B.Phillipp, H.Sahm, and L.Eggeling (1998).
Different modes of diaminopimelate synthesis and their role in cell wall integrity: a study with Corynebacterium glutamicum.
  J Bacteriol, 180, 3159-3165.  
  9440522 G.D.Dotson, I.A.Kaltashov, R.J.Cotter, and C.R.Raetz (1998).
Expression cloning of a Pseudomonas gene encoding a hydroxydecanoyl-acyl carrier protein-dependent UDP-GlcNAc acyltransferase.
  J Bacteriol, 180, 330-337.  
9671504 T.W.Beaman, J.S.Blanchard, and S.L.Roderick (1998).
The conformational change and active site structure of tetrahydrodipicolinate N-succinyltransferase.
  Biochemistry, 37, 10363-10369.
PDB codes: 2tdt 3tdt
9578552 T.W.Beaman, M.Sugantino, and S.L.Roderick (1998).
Structure of the hexapeptide xenobiotic acetyltransferase from Pseudomonas aeruginosa.
  Biochemistry, 37, 6689-6696.
PDB codes: 1xat 2xat
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.

 

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