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PDBsum entry 1cs0

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1cs0
Jmol
Contents
Protein chains
1058 a.a. *
379 a.a. *
Ligands
PO4 ×5
ADP ×8
ORN ×4
NET ×4
Metals
__K ×33
_CL ×29
_MN ×12
Waters ×4176
* Residue conservation analysis
PDB id:
1cs0
Name: Ligase
Title: Crystal structure of carbamoyl phosphate synthetase complexe cys269 in the small subunit with the tetrahedral mimic l-gl gamma-semialdehyde
Structure: Carbamoyl phosphate synthetase: large subunit. Chain: a, c, e, g. Engineered: yes. Carbamoyl phosphate synthetase: small subunit. Chain: b, d, f, h. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.186     R-free:   0.242
Authors: J.B.Thoden,X.Huang,F.M.Raushel,H.M.Holden
Key ref:
J.B.Thoden et al. (1999). The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway. Biochemistry, 38, 16158-16166. PubMed id: 10587438 DOI: 10.1021/bi991741j
Date:
16-Aug-99     Release date:   10-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00968  (CARB_ECOLI) -  Carbamoyl-phosphate synthase large chain
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1073 a.a.
1058 a.a.
Protein chains
Pfam   ArchSchema ?
P0A6F1  (CARA_ECOLI) -  Carbamoyl-phosphate synthase small chain
Seq:
Struc:
382 a.a.
379 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.6.3.5.5  - Carbamoyl-phosphate synthase (glutamine-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Pyrimidine Biosynthesis
      Reaction: 2 ATP + L-glutamine + HCO3- + H2O = 2 ADP + phosphate + L-glutamate + carbamoyl phosphate
2 × ATP
+
L-glutamine
Bound ligand (Het Group name = ORN)
matches with 90.00% similarity
+ HCO(3)(-)
+ H(2)O
=
2 × ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
+ L-glutamate
+ carbamoyl phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     metabolic process   12 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi991741j Biochemistry 38:16158-16166 (1999)
PubMed id: 10587438  
 
 
The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway.
J.B.Thoden, X.Huang, F.M.Raushel, H.M.Holden.
 
  ABSTRACT  
 
Carbamoyl phosphate synthetase (CPS) plays a key role in both arginine and pyrimidine biosynthesis by catalyzing the production of carbamoyl phosphate. The enzyme from Escherichi coli consists of two polypeptide chains referred to as the small and large subunits. On the basis of both amino acid sequence analyses and X-ray structural studies, it is known that the small subunit belongs to the Triad or Type I class of amidotransferases, all of which contain a cysteine-histidine (Cys269 and His353) couple required for activity. The hydrolysis of glutamine by the small subunit has been proposed to occur via two tetrahedral intermediates and a glutamyl-thioester moiety. Here, we describe the three-dimensional structures of the C269S/glutamine and CPS/glutamate gamma-semialdehyde complexes, which serve as mimics for the Michaelis complex and the tetrahedral intermediates, respectively. In conjunction with the previously solved glutamyl-thioester intermediate complex, the stereochemical course of glutamine hydrolysis in CPS has been outlined. Specifically, attack by the thiolate of Cys269 occurs at the Si face of the carboxamide group of the glutamine substrate leading to a tetrahedral intermediate with an S-configuration. Both the backbone amide groups of Gly241 and Leu270, and O(gamma) of Ser47 play key roles in stabilizing the developing oxyanion. Collapse of the tetrahedral intermediate leads to formation of the glutamyl-thioester intermediate, which is subsequently attacked at the Si face by an activated water molecule positioned near His353. The results described here serve as a paradigm for other members of the Triad class of amidotranferases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20187643 L.Lund, Y.Fan, Q.Shao, Y.Q.Gao, and F.M.Raushel (2010).
Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation.
  J Am Chem Soc, 132, 3870-3878.  
19569682 Y.Fan, L.Lund, Q.Shao, Y.Q.Gao, and F.M.Raushel (2009).
A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase.
  J Am Chem Soc, 131, 10211-10219.  
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.  
18597481 M.Morar, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2008).
Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation.
  Biochemistry, 47, 7816-7830.
PDB code: 3d54
17209549 J.L.Johnson, J.K.West, A.D.Nelson, and G.D.Reinhart (2007).
Resolving the fluorescence response of Escherichia coli carbamoyl phosphate synthetase: mapping intra- and intersubunit conformational changes.
  Biochemistry, 46, 387-397.  
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
15576558 M.Kothe, C.Purcarea, H.I.Guy, D.R.Evans, and S.G.Powers-Lee (2005).
Direct demonstration of carbamoyl phosphate formation on the C-terminal domain of carbamoyl phosphate synthetase.
  Protein Sci, 14, 37-44.  
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.  
15849257 R.E.Amaro, R.S.Myers, V.J.Davisson, and Z.A.Luthey-Schulten (2005).
Structural elements in IGP synthase exclude water to optimize ammonia transfer.
  Biophys J, 89, 475-487.  
16030023 T.Raschle, N.Amrhein, and T.B.Fitzpatrick (2005).
On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis.
  J Biol Chem, 280, 32291-32300.  
15157079 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (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.
PDB code: 1s1m
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
12799468 R.Amaro, E.Tajkhorshid, and Z.Luthey-Schulten (2003).
Developing an energy landscape for the novel function of a (beta/alpha)8 barrel: ammonia conduction through HisF.
  Proc Natl Acad Sci U S A, 100, 7599-7604.  
11729189 B.W.Miles, J.B.Thoden, H.M.Holden, and F.M.Raushel (2002).
Inactivation of the amidotransferase activity of carbamoyl phosphate synthetase by the antibiotic acivicin.
  J Biol Chem, 277, 4368-4373.
PDB code: 1kee
11953431 H.Li, T.J.Ryan, K.J.Chave, and P.Van Roey (2002).
Three-dimensional structure of human gamma -glutamyl hydrolase. A class I glatamine amidotransferase adapted for a complex substate.
  J Biol Chem, 277, 24522-24529.
PDB code: 1l9x
12130656 J.B.Thoden, X.Huang, F.M.Raushel, and H.M.Holden (2002).
Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia.
  J Biol Chem, 277, 39722-39727.
PDB code: 1m6v
11933259 P.T.Rajagopalan, and S.J.Benkovic (2002).
Preorganization and protein dynamics in enzyme catalysis.
  Chem Rec, 2, 24-36.  
11371633 G.Spraggon, C.Kim, X.Nguyen-Huu, M.C.Yee, C.Yanofsky, and S.E.Mills (2001).
The structures of anthranilate synthase of Serratia marcescens crystallized in the presence of (i) its substrates, chorismate and glutamine, and a product, glutamate, and (ii) its end-product inhibitor, L-tryptophan.
  Proc Natl Acad Sci U S A, 98, 6021-6026.
PDB codes: 1i7q 1i7s
11119647 M.M.Horvath, and N.V.Grishin (2001).
The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily.
  Proteins, 42, 230-236.  
10852731 M.A.Rishavy, W.W.Cleland, and C.J.Lusty (2000).
15N isotope effects in glutamine hydrolysis catalyzed by carbamyl phosphate synthetase: evidence for a tetrahedral intermediate in the mechanism.
  Biochemistry, 39, 7309-7315.  
10966576 M.Y.Galperin, and N.V.Grishin (2000).
The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
  Proteins, 41, 238-247.  
10828939 T.C.Bruice, and S.J.Benkovic (2000).
Chemical basis for enzyme catalysis.
  Biochemistry, 39, 6267-6274.  
10727215 X.Huang, and F.M.Raushel (2000).
An engineered blockage within the ammonia tunnel of carbamoyl phosphate synthetase prevents the use of glutamine as a substrate but not ammonia.
  Biochemistry, 39, 3240-3247.  
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.