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PDBsum entry 1s1m

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1s1m
Jmol
Contents
Protein chains
534 a.a. *
Ligands
SO4 ×4
MPD ×2
Metals
_MG ×4
IOD ×16
Waters ×549
* Residue conservation analysis
PDB id:
1s1m
Name: Ligase
Title: Crystal structure of e. Coli ctp synthetase
Structure: Ctp synthase. Chain: a, b. Synonym: utp--ammonia ligase, ctp synthetase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: pyrg, b2780, c3345, z4095, ecs3640, sf2795, s2989. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.214     R-free:   0.281
Authors: J.A.Endrizzi,H.Kim,P.M.Anderson,E.P.Baldwin
Key ref:
J.A.Endrizzi et al. (2004). Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets. Biochemistry, 43, 6447-6463. PubMed id: 15157079 DOI: 10.1021/bi0496945
Date:
06-Jan-04     Release date:   15-Jun-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A7E5  (PYRG_ECOLI) -  CTP synthase
Seq:
Struc:
 
Seq:
Struc:
545 a.a.
534 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.4.2  - Ctp synthase (glutamine hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + UTP + L-glutamine = ADP + phosphate + CTP + L-glutamate
ATP
+ UTP
+ L-glutamine
= ADP
+ phosphate
+ CTP
+ L-glutamate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     'de novo' CTP biosynthetic process   4 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi0496945 Biochemistry 43:6447-6463 (2004)
PubMed id: 15157079  
 
 
Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets.
J.A.Endrizzi, H.Kim, P.M.Anderson, E.P.Baldwin.
 
  ABSTRACT  
 
Cytidine triphosphate synthetases (CTPSs) produce CTP from UTP and glutamine, and regulate intracellular CTP levels through interactions with the four ribonucleotide triphosphates. We solved the 2.3-A resolution crystal structure of Escherichia coli CTPS using Hg-MAD phasing. The structure reveals a nearly symmetric 222 tetramer, in which each bifunctional monomer contains a dethiobiotin synthetase-like amidoligase N-terminal domain and a Type 1 glutamine amidotransferase C-terminal domain. For each amidoligase active site, essential ATP- and UTP-binding surfaces are contributed by three monomers, suggesting that activity requires tetramer formation, and that a nucleotide-dependent dimer-tetramer equilibrium contributes to the observed positive cooperativity. A gated channel that spans 25 A between the glutamine hydrolysis and amidoligase active sites provides a path for ammonia diffusion. The channel is accessible to solvent at the base of a cleft adjoining the glutamine hydrolysis active site, providing an entry point for exogenous ammonia. Guanine nucleotide binding sites of structurally related GTPases superimpose on this cleft, providing insights into allosteric regulation by GTP. Mutations that confer nucleoside drug resistance and release CTP inhibition map to a pocket that neighbors the UTP-binding site and can accommodate a pyrimidine ring. Its location suggests that competitive feedback inhibition is affected via a distinct product/drug binding site that overlaps the substrate triphosphate binding site. Overall, the E. coli structure provides a framework for homology modeling of other CTPSs and structure-based design of anti-CTPS therapeutics.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21254152 J.L.Liu (2011).
The enigmatic cytoophidium: Compartmentation of CTP synthase via filament formation.
  Bioessays, 33, 159-164.  
20639870 M.Ingerson-Mahar, A.Briegel, J.N.Werner, G.J.Jensen, and Z.Gitai (2010).
The metabolic enzyme CTP synthase forms cytoskeletal filaments.
  Nat Cell Biol, 12, 739-746.  
19270703 N.LaRonde-LeBlanc, M.Resto, and B.Gerratana (2009).
Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
  Nat Struct Mol Biol, 16, 421-429.
PDB code: 3dla
18458150 E.J.Hart, and S.G.Powers-Lee (2008).
Mutation analysis of carbamoyl phosphate synthetase: does the structurally conserved glutamine amidotransferase triad act as a functional dyad?
  Protein Sci, 17, 1120-1128.  
18003612 F.A.Lunn, J.E.Macdonnell, and S.L.Bearne (2008).
Structural Requirements for the Activation of Escherichia coli CTP Synthase by the Allosteric Effector GTP Are Stringent, but Requirements for Inhibition Are Lax.
  J Biol Chem, 283, 2010-2020.  
18988211 S.D.Taylor, F.A.Lunn, and S.L.Bearne (2008).
Ground state, intermediate, and multivalent nucleotide analogue inhibitors of cytidine 5'-triphosphate synthase.
  ChemMedChem, 3, 1853-1857.  
18004774 Y.Agari, S.Sato, T.Wakamatsu, Y.Bessho, A.Ebihara, S.Yokoyama, S.Kuramitsu, and A.Shinkai (2008).
X-ray crystal structure of a hypothetical Sua5 protein from Sulfolobus tokodaii strain 7.
  Proteins, 70, 1108-1111.
PDB code: 2eqa
18439916 Y.F.Chang, and G.M.Carman (2008).
CTP synthetase and its role in phospholipid synthesis in the yeast Saccharomyces cerevisiae.
  Prog Lipid Res, 47, 333-339.  
17331943 A.Fijolek, A.Hofer, and L.Thelander (2007).
Expression, purification, characterization, and in vivo targeting of trypanosome CTP synthetase for treatment of African sleeping sickness.
  J Biol Chem, 282, 11858-11865.  
17210578 C.Evrin, M.Straut, N.Slavova-Azmanova, N.Bucurenci, A.Onu, L.Assairi, M.Ionescu, N.Palibroda, O.Bârzu, and A.M.Gilles (2007).
Regulatory mechanisms differ in UMP kinases from gram-negative and gram-positive bacteria.
  J Biol Chem, 282, 7242-7253.  
17189248 M.G.Choi, and G.M.Carman (2007).
Phosphorylation of human CTP synthetase 1 by protein kinase A: identification of Thr455 as a major site of phosphorylation.
  J Biol Chem, 282, 5367-5377.  
17681942 M.J.Higgins, P.R.Graves, and L.M.Graves (2007).
Regulation of human cytidine triphosphate synthetase 1 by glycogen synthase kinase 3.
  J Biol Chem, 282, 29493-29503.  
17600152 O.Braun, M.Knipp, S.Chesnov, and M.Vasák (2007).
Specific reactions of S-nitrosothiols with cysteine hydrolases: A comparative study between dimethylargininase-1 and CTP synthetase.
  Protein Sci, 16, 1522-1534.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
17463002 Y.F.Chang, S.S.Martin, E.P.Baldwin, and G.M.Carman (2007).
Phosphorylation of human CTP synthetase 1 by protein kinase C: identification of Ser(462) and Thr(455) as major sites of phosphorylation.
  J Biol Chem, 282, 17613-17622.  
16756505 N.G.Richards, and M.S.Kilberg (2006).
Asparagine synthetase chemotherapy.
  Annu Rev Biochem, 75, 629-654.  
  16820675 P.Kursula, S.Flodin, M.Ehn, M.Hammarström, H.Schüler, P.Nordlund, and P.Stenmark (2006).
Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 613-617.
PDB codes: 2c5m 2vo1
16179339 G.S.Han, A.Sreenivas, M.G.Choi, Y.F.Chang, S.S.Martin, E.P.Baldwin, and G.M.Carman (2005).
Expression of Human CTP synthetase in Saccharomyces cerevisiae reveals phosphorylation by protein kinase A.
  J Biol Chem, 280, 38328-38336.  
16216072 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (2005).
Mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a CTP-inhibited complex.
  Biochemistry, 44, 13491-13499.
PDB code: 2ad5
15670165 M.Willemoës, A.Mølgaard, E.Johansson, and J.Martinussen (2005).
Lid L11 of the glutamine amidotransferase domain of CTP synthase mediates allosteric GTP activation of glutaminase activity.
  FEBS J, 272, 856-864.  
15511226 F.A.Lunn, and S.L.Bearne (2004).
Alternative substrates for wild-type and L109A E. coli CTP synthases: kinetic evidence for a constricted ammonia tunnel.
  Eur J Biochem, 271, 4204-4212.  
15296735 M.Goto, R.Omi, N.Nakagawa, I.Miyahara, and K.Hirotsu (2004).
Crystal structures of CTP synthetase reveal ATP, UTP, and glutamine binding sites.
  Structure, 12, 1413-1423.
PDB codes: 1vcm 1vcn 1vco
7797479 W.L.Yang, and G.M.Carman (1995).
Phosphorylation of CTP synthetase from Saccharomyces cerevisiae by protein kinase C.
  J Biol Chem, 270, 14983-14988.  
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.