PDBsum entry 1oy0

Go to PDB code: 
protein metals Protein-protein interface(s) links
Transferase PDB id
Protein chains
248 a.a. *
_MG ×5
Waters ×105
* Residue conservation analysis
PDB id:
Name: Transferase
Title: The crystal structure of the first enzyme of pantothenate bi pathway, ketopantoate hydroxymethyltransferase from mycobac tuberculosis shows a decameric assembly and terminal helix-
Structure: Ketopantoate hydroxymethyltransferase. Chain: a, b, c, d, e. Synonym: 3-methyl-2-oxobutanoate hydroxymethyltransferase. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: panb. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Decamer (from PDB file)
2.80Å     R-factor:   0.239     R-free:   0.275
Authors: B.N.Chaudhuri,M.R.Sawaya,C.Y.Kim,G.S.Waldo,M.S.Park,T.C.Terw T.O.Yeates,Tb Structural Genomics Consortium (Tbsgc)
Key ref:
B.N.Chaudhuri et al. (2003). The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis. Structure, 11, 753-764. PubMed id: 12842039 DOI: 10.1016/S0969-2126(03)00106-0
03-Apr-03     Release date:   15-Jul-03    
Go to PROCHECK summary

Protein chains
P9WIL7  (PANB_MYCTU) -  3-methyl-2-oxobutanoate hydroxymethyltransferase
281 a.a.
248 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 3-methyl-2-oxobutanoate hydroxymethyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Coenzyme A Biosynthesis (early stages)
      Reaction: 5,10-methylenetetrahydrofolate + 3-methyl-2-oxobutanoate + H2O = tetrahydrofolate + 2-dehydropantoate
+ 3-methyl-2-oxobutanoate
+ H(2)O
= tetrahydrofolate
+ 2-dehydropantoate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   2 terms 
  Biological process     growth   2 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1016/S0969-2126(03)00106-0 Structure 11:753-764 (2003)
PubMed id: 12842039  
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, T.O.Yeates.
Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate, which is a precursor to coenzyme A and is required for penicillin biosynthesis. The crystal structure of KPHMT from Mycobacterium tuberculosis was determined by the single anomalous substitution (SAS) method at 2.8 A resolution. KPHMT adopts a structure that is a variation on the (beta/alpha) barrel fold, with a metal binding site proximal to the presumed catalytic site. The protein forms a decameric complex, with subunits in opposing pentameric rings held together by a swapping of their C-terminal alpha helices. The structure reveals KPHMT's membership in a small, recently discovered group of (beta/alpha) barrel enzymes that employ domain swapping to form a variety of oligomeric assemblies. The apparent conservation of certain detailed structural characteristics suggests that KPHMT is distantly related by divergent evolution to enzymes in unrelated pathways, including isocitrate lyase and phosphoenolpyruvate mutase.
  Selected figure(s)  
Figure 5.
Figure 5. A Comparison of the Metal Coordination Sites in KPHMT, PEPM, and ICL(A) KPHMT active site residues that are coordinated by a metal ion.(B) The PEPM active site with oxalate bound (Protein Data Bank code 1pym).(C) The ICL active site with glyoxylate bound (Protein Data Bank code 1f8i). The two metal ion-coordinating residues (Asp101 and Glu133) and the h2 helix in KPHMT have corresponding counterparts in PEPM and ICL. In all panels, the oxygen and nitrogen atoms are shown as gray and black spheres, respectively, with the magnesium ion shown as the larger black sphere. Hydrogen bonds are shown as dashed lines. Note that the N terminus of the h2 helix is in 3[10] conformation in KPHMT, whereas it is a helical in PEPM and ICL.
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 753-764) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21169697 R.Talon, R.Kahn, M.A.Durá, O.Maury, F.M.Vellieux, B.Franzetti, and E.Girard (2011).
Using lanthanoid complexes to phase large macromolecular assemblies.
  J Synchrotron Radiat, 18, 74-78.  
20203624 F.Striebel, M.Hunkeler, H.Summer, and E.Weber-Ban (2010).
The mycobacterial Mpa-proteasome unfolds and degrades pupylated substrates by engaging Pup's N-terminus.
  EMBO J, 29, 1262-1271.  
18081320 B.C.Narayanan, W.Niu, Y.Han, J.Zou, P.S.Mariano, D.Dunaway-Mariano, and O.Herzberg (2008).
Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily.
  Biochemistry, 47, 167-182.
PDB code: 3b8i
18433062 C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, and S.H.Chou (2008).
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
  Proteins, 73, 362-371.
PDB code: 2ze3
17082771 M.J.Pearce, P.Arora, R.A.Festa, S.M.Butler-Wu, R.S.Gokhale, and K.H.Darwin (2006).
Identification of substrates of the Mycobacterium tuberculosis proteasome.
  EMBO J, 25, 5423-5432.  
16478688 V.L.Arcus, J.S.Lott, J.M.Johnston, and E.N.Baker (2006).
The potential impact of structural genomics on tuberculosis drug discovery.
  Drug Discov Today, 11, 28-34.  
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.