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PDBsum entry 1iho

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protein ligands Protein-protein interface(s) links
Ligase PDB id
1iho
Jmol
Contents
Protein chains
282 a.a. *
Ligands
TRS
EDO ×2
Waters ×614
* Residue conservation analysis
PDB id:
1iho
Name: Ligase
Title: Crystal apo-structure of pantothenate synthetase from e. Col
Structure: Pantoate--beta-alanine ligase. Chain: a, b. Synonym: pantothenate synthetase, pantoate activating enzym engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: panc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.211     R-free:   0.254
Authors: F.Von Delft,A.Lewendon,V.Dhanaraj,T.L.Blundell,C.Abell,A.Smi
Key ref:
F.von Delft et al. (2001). The crystal structure of E. coli pantothenate synthetase confirms it as a member of the cytidylyltransferase superfamily. Structure, 9, 439-450. PubMed id: 11377204
Date:
19-Apr-01     Release date:   30-May-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P31663  (PANC_ECOLI) -  Pantothenate synthetase
Seq:
Struc:
283 a.a.
282 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.1  - Pantoate--beta-alanine ligase (AMP-forming).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Coenzyme A Biosynthesis (early stages)
      Reaction: ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
ATP
+
(R)-pantoate
Bound ligand (Het Group name = TRS)
matches with 50.00% similarity
+ beta-alanine
= AMP
+ diphosphate
+ (R)-pantothenate
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     biosynthetic process   3 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
Structure 9:439-450 (2001)
PubMed id: 11377204  
 
 
The crystal structure of E. coli pantothenate synthetase confirms it as a member of the cytidylyltransferase superfamily.
F.von Delft, A.Lewendon, V.Dhanaraj, T.L.Blundell, C.Abell, A.G.Smith.
 
  ABSTRACT  
 
BACKGROUND: Pantothenate synthetase (EC 6.3.2.1) is the last enzyme of the pathway of pantothenate (vitamin B(5)) synthesis. It catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction. RESULTS: We describe the overexpression, purification, and crystal structure of recombinant pantothenate synthetase from E. coli. The structure was solved by a selenomethionine multiwavelength anomalous dispersion experiment and refined against native data to a final R(cryst) of 22.6% (R(free) = 24.9%) at 1.7 A resolution. The enzyme is dimeric, with two well-defined domains per protomer: the N-terminal domain, a Rossmann fold, contains the active site cavity, with the C-terminal domain forming a hinged lid. CONCLUSIONS: The N-terminal domain is structurally very similar to class I aminoacyl-tRNA synthetases and is thus a member of the cytidylyltransferase superfamily. This relationship has been used to suggest the location of the ATP and pantoate binding sites and the nature of hinge bending that leads to the ternary enzyme-pantoate-ATP complex.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21425349 Y.S.Tan, G.Fuentes, and C.Verma (2011).
A comparison of the dynamics of pantothenate synthetase from M. tuberculosis and E. coli: Computational studies.
  Proteins, 79, 1715-1727.  
20059543 K.S.Chakrabarti, K.G.Thakur, B.Gopal, and S.P.Sarma (2010).
X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate.
  FEBS J, 277, 697-712.
PDB code: 3guz
19505149 F.Fan, and J.S.Blanchard (2009).
Toward the catalytic mechanism of a cysteine ligase (MshC) from Mycobacterium smegmatis: an enzyme involved in the biosynthetic pathway of mycothiol.
  Biochemistry, 48, 7150-7159.  
18645235 C.Dumas, and A.van der Lee (2008).
Macromolecular structure solution by charge flipping.
  Acta Crystallogr D Biol Crystallogr, 64, 864-873.  
18726075 E.Chakauya, K.M.Coxon, M.Wei, M.V.Macdonald, T.Barsby, C.Abell, and A.G.Smith (2008).
Towards engineering increased pantothenate (vitamin B(5)) levels in plants.
  Plant Mol Biol, 68, 493-503.  
18422645 S.Ronconi, R.Jonczyk, and U.Genschel (2008).
A novel isoform of pantothenate synthetase in the Archaea.
  FEBS J, 275, 2754-2764.  
17898893 G.L.Holliday, J.M.Thornton, A.Marquet, A.G.Smith, F.Rébeillé, R.Mendel, H.L.Schubert, A.D.Lawrence, and M.J.Warren (2007).
Evolution of enzymes and pathways for the biosynthesis of cofactors.
  Nat Prod Rep, 24, 972-987.  
  17554169 J.Seetharamappa, M.Oke, H.Liu, S.A.McMahon, K.A.Johnson, L.Carter, M.Dorward, M.Zawadzki, I.M.Overton, C.A.van Niekirk, S.Graham, C.H.Botting, G.L.Taylor, M.F.White, G.J.Barton, P.J.Coote, and J.H.Naismith (2007).
Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 488-491.  
16990935 K.L.Tuck, S.A.Saldanha, L.M.Birch, A.G.Smith, and C.Abell (2006).
The design and synthesis of inhibitors of pantothenate synthetase.
  Org Biomol Chem, 4, 3598-3610.  
17040917 R.Jonczyk, and U.Genschel (2006).
Molecular adaptation and allostery in plant pantothenate synthetases.
  J Biol Chem, 281, 37435-37446.  
15572774 E.Blanc, P.Roversi, C.Vonrhein, C.Flensburg, S.M.Lea, and G.Bricogne (2004).
Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT.
  Acta Crystallogr D Biol Crystallogr, 60, 2210-2221.  
14675432 H.H.Ottenhof, J.L.Ashurst, H.M.Whitney, S.A.Saldanha, F.Schmitzberger, H.S.Gweon, T.L.Blundell, C.Abell, and A.G.Smith (2004).
Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants.
  Plant J, 37, 61-72.  
14523010 C.Y.Lai, and J.E.Cronan (2003).
Beta-ketoacyl-acyl carrier protein synthase III (FabH) is essential for bacterial fatty acid synthesis.
  J Biol Chem, 278, 51494-51503.  
12906829 F.von Delft, T.Inoue, S.A.Saldanha, H.H.Ottenhof, F.Schmitzberger, L.M.Birch, V.Dhanaraj, M.Witty, A.G.Smith, T.L.Blundell, and C.Abell (2003).
Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites.
  Structure, 11, 985-996.
PDB code: 1m3u
12906824 N.Manoj, E.Strauss, T.P.Begley, and S.E.Ealick (2003).
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
  Structure, 11, 927-936.
PDB code: 1p9o
12717031 S.Wang, and D.Eisenberg (2003).
Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate.
  Protein Sci, 12, 1097-1108.
PDB codes: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o
12837781 T.Izard (2003).
A novel adenylate binding site confers phosphopantetheine adenylyltransferase interactions with coenzyme A.
  J Bacteriol, 185, 4074-4080.
PDB code: 1h1t
12810729 V.Saridakis, and E.F.Pai (2003).
Mutational, structural, and kinetic studies of the ATP-binding site of Methanobacterium thermoautotrophicum nicotinamide mononucleotide adenylyltransferase.
  J Biol Chem, 278, 34356-34363.
PDB codes: 1m8f 1m8g 1m8j 1m8k
11976504 A.R.Kwon, B.I.Lee, B.W.Han, H.J.Ahn, J.K.Yang, H.J.Yoon, and S.W.Suh (2002).
Crystallization and preliminary X-ray crystallographic analysis of aspartate 1-decarboxylase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 58, 861-863.  
12012333 L.Aravind, V.Anantharaman, and E.V.Koonin (2002).
Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA.
  Proteins, 48, 1.  
11751893 S.Garavaglia, I.D'Angelo, M.Emanuelli, F.Carnevali, F.Pierella, G.Magni, and M.Rizzi (2002).
Structure of human NMN adenylyltransferase. A key nuclear enzyme for NAD homeostasis.
  J Biol Chem, 277, 8524-8530.
PDB code: 1kku
12140293 T.Kupke (2002).
Molecular characterization of the 4'-phosphopantothenoylcysteine synthetase domain of bacterial dfp flavoproteins.
  J Biol Chem, 277, 36137-36145.  
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.