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PDBsum entry 1bxr

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Amidotransferase PDB id
1bxr
Jmol
Contents
Protein chains
1073 a.a. *
379 a.a. *
Ligands
ANP ×8
ORN ×4
NET ×4
Metals
__K ×19
_MN ×13
_CL ×14
Waters ×3242
* Residue conservation analysis
PDB id:
1bxr
Name: Amidotransferase
Title: Structure of carbamoyl phosphate synthetase complexed with t analog amppnp
Structure: Carbamoyl-phosphate synthase. Chain: a, c, e, g. Engineered: yes. Carbamoyl-phosphate synthase. Chain: b, d, f, h. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.195    
Authors: J.B.Thoden,G.Wesenberg,F.M.Raushel,H.M.Holden
Key ref:
J.B.Thoden et al. (1999). Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding. Biochemistry, 38, 2347-2357. PubMed id: 10029528 DOI: 10.1021/bi982517h
Date:
08-Oct-98     Release date:   20-Apr-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.
1073 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 = ANP)
matches with 81.25% similarity
+ phosphate
+ 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/bi982517h Biochemistry 38:2347-2357 (1999)
PubMed id: 10029528  
 
 
Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding.
J.B.Thoden, G.Wesenberg, F.M.Raushel, H.M.Holden.
 
  ABSTRACT  
 
Carbamoyl phosphate synthetase (CPS) catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The catalytic mechanism of the enzyme occurs through three highly reactive intermediates: carboxyphosphate, ammonia, and carbamate. As isolated from Escherichia coli, CPS is an alpha, beta-heterodimeric protein with its three active sites separated by nearly 100 A. In addition, there are separate binding sites for the allosteric regulators, ornithine, and UMP. Given the sizable distances between the three active sites and the allosteric-binding pockets, it has been postulated that domain movements play key roles for intramolecular communication. Here we describe the structure of CPS from E. coli where, indeed, such a domain movement has occurred in response to nucleotide binding. Specifically, the protein was crystallized in the presence of a nonhydrolyzable analogue, AMPPNP, and its structure determined to 2.1 A resolution by X-ray crystallographic analysis. The B-domain of the carbamoyl phosphate synthetic component of the large subunit closes down over the active-site pocket such that some atoms move by more than 7 A relative to that observed in the original structure. The trigger for this movement resides in the hydrogen-bonding interactions between two backbone amide groups (Gly 721 and Gly 722) and the beta- and gamma-phosphate groups of the nucleotide triphosphate. Gly 721 and Gly 722 are located in a Type III' reverse turn, and this type of secondary structural motif is also observed in D-alanine:D-alanine ligase and glutathione synthetase, both of which belong to the "ATP-grasp" superfamily of proteins. Details concerning the geometries of the two active sites contained within the large subunit of CPS are described.
 

Literature references that cite this PDB file's key reference Google scholar

  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.  
19142949 M.Weisel, E.Proschak, J.M.Kriegl, and G.Schneider (2009).
Form follows function: shape analysis of protein cavities for receptor-based drug design.
  Proteomics, 9, 451-459.  
18725455 I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, and G.L.Waldrop (2008).
Structural evidence for substrate-induced synergism and half-sites reactivity in biotin carboxylase.
  Protein Sci, 17, 1706-1718.
PDB codes: 2c00 2j9g 2vpq 2vqd 2vr1
18271571 S.O.Nilsson Lill, J.Gao, and G.L.Waldrop (2008).
Molecular dynamics simulations of biotin carboxylase.
  J Phys Chem B, 112, 3149-3156.  
18069798 Y.Zhang, R.H.White, and S.E.Ealick (2008).
Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
  Biochemistry, 47, 205-217.
PDB codes: 2r7k 2r7l 2r7m 2r7n 2r84 2r85 2r86 2r87
17983264 C.H.Yeang, and D.Haussler (2007).
Detecting coevolution in and among protein domains.
  PLoS Comput Biol, 3, e211.  
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.  
17717183 M.St Maurice, L.Reinhardt, K.H.Surinya, P.V.Attwood, J.C.Wallace, W.W.Cleland, and I.Rayment (2007).
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
  Science, 317, 1076-1079.
PDB code: 2qf7
17951049 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Conformational changes in ammonia-channeling glutamine amidotransferases.
  Curr Opin Struct Biol, 17, 653-664.  
14718657 M.Kothe, and S.G.Powers-Lee (2004).
Nucleotide recognition in the ATP-grasp protein carbamoyl phosphate synthetase.
  Protein Sci, 13, 466-475.  
14563877 C.Merlin, M.Masters, S.McAteer, and A.Coulson (2003).
Why is carbonic anhydrase essential to Escherichia coli?
  J Bacteriol, 185, 6415-6424.  
11953435 J.B.Thoden, S.M.Firestine, S.J.Benkovic, and H.M.Holden (2002).
PurT-encoded glycinamide ribonucleotide transformylase. Accommodation of adenosine nucleotide analogs within the active site.
  J Biol Chem, 277, 23898-23908.
PDB codes: 1kj8 1kj9 1kji 1kjj 1kjq
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
11574542 A.Ahuja, C.Purcarea, H.I.Guy, and D.R.Evans (2001).
A novel carbamoyl-phosphate synthetase from Aquifex aeolicus.
  J Biol Chem, 276, 45694-45703.  
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
11208798 T.J.Klem, Y.Chen, and V.J.Davisson (2001).
Subunit interactions and glutamine utilization by Escherichia coli imidazole glycerol phosphate synthase.
  J Bacteriol, 183, 989-996.  
10821865 J.B.Thoden, C.Z.Blanchard, H.M.Holden, and G.L.Waldrop (2000).
Movement of the biotin carboxylase B-domain as a result of ATP binding.
  J Biol Chem, 275, 16183-16190.
PDB codes: 1dv1 1dv2
10913290 J.B.Thoden, S.Firestine, A.Nixon, S.J.Benkovic, and H.M.Holden (2000).
Molecular structure of Escherichia coli PurT-encoded glycinamide ribonucleotide transformylase.
  Biochemistry, 39, 8791-8802.
PDB codes: 1eyz 1ez1
10625475 M.A.Joyce, M.E.Fraser, M.N.James, W.A.Bridger, and W.T.Wolodko (2000).
ADP-binding site of Escherichia coli succinyl-CoA synthetase revealed by x-ray crystallography.
  Biochemistry, 39, 17-25.
PDB codes: 1cqi 1cqj
10497179 A.Hewagama, H.I.Guy, J.F.Vickrey, and D.R.Evans (1999).
Functional linkage between the glutaminase and synthetase domains of carbamoyl-phosphate synthetase. Role of serine 44 in carbamoyl-phosphate synthetase-aspartate carbamoyltransferase-dihydroorotase (cad).
  J Biol Chem, 274, 28240-28245.  
10387030 F.M.Raushel, J.B.Thoden, and H.M.Holden (1999).
The amidotransferase family of enzymes: molecular machines for the production and delivery of ammonia.
  Biochemistry, 38, 7891-7899.  
10587438 J.B.Thoden, X.Huang, F.M.Raushel, and H.M.Holden (1999).
The small subunit of carbamoyl phosphate synthetase: snapshots along the reaction pathway.
  Biochemistry, 38, 16158-16166.
PDB codes: 1c30 1c3o 1cs0
10587437 T.M.Larsen, S.K.Boehlein, S.M.Schuster, N.G.Richards, J.B.Thoden, H.M.Holden, and I.Rayment (1999).
Three-dimensional structure of Escherichia coli asparagine synthetase B: a short journey from substrate to product.
  Biochemistry, 38, 16146-16157.
PDB code: 1ct9
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 codes are shown on the right.