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PDBsum entry 1cli

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protein ligands Protein-protein interface(s) links
Ligase PDB id
1cli
Jmol
Contents
Protein chains
341 a.a. *
Ligands
SO4 ×4
Waters ×503
* Residue conservation analysis
PDB id:
1cli
Name: Ligase
Title: X-ray crystal structure of aminoimidazole ribonucleotide syn (purm), from the e. Coli purine biosynthetic pathway, at 2. Resolution
Structure: Protein (phosphoribosyl-aminoimidazole synthetase chain: a, b, c, d. Engineered: yes. Other_details: sulfate bindng
Source: Escherichia coli. Organism_taxid: 562. Cellular_location: cytoplasm. Gene: purm. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Expression_system_cell_line: bl21. Expression_system_cell: bl21. Other_details: cloned gene
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.192     R-free:   0.264
Authors: C.Li,T.J.Kappock,J.Stubbe,T.M.Weaver,S.E.Ealick
Key ref:
C.Li et al. (1999). X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution. Structure, 7, 1155-1166. PubMed id: 10508786 DOI: 10.1016/S0969-2126(99)80182-8
Date:
28-Apr-99     Release date:   06-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08178  (PUR5_ECOLI) -  Phosphoribosylformylglycinamidine cyclo-ligase
Seq:
Struc:
345 a.a.
341 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.3.1  - Phosphoribosylformylglycinamidine cyclo-ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Purine Biosynthesis (early stages)
      Reaction: ATP + 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine = ADP + phosphate + 5-amino-1-(5-phospho-D-ribosyl)imidazole
ATP
+ 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine
= ADP
+ phosphate
+ 5-amino-1-(5-phospho-D-ribosyl)imidazole
      Cofactor: Magnesium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     purine nucleotide biosynthetic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(99)80182-8 Structure 7:1155-1166 (1999)
PubMed id: 10508786  
 
 
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution.
C.Li, T.J.Kappock, J.Stubbe, T.M.Weaver, S.E.Ealick.
 
  ABSTRACT  
 
BACKGROUND: The purine biosynthetic pathway in procaryotes enlists eleven enzymes, six of which use ATP. Enzymes 5 and 6 of this pathway, formylglycinamide ribonucleotide (FGAR) amidotransferase (PurL) and aminoimidazole ribonucleotide (AIR) synthetase (PurM) utilize ATP to activate the oxygen of an amide within their substrate toward nucleophilic attack by a nitrogen. AIR synthetase uses the product of PurL, formylglycinamidine ribonucleotide (FGAM) and ATP to make AIR, ADP and P(i). RESULTS: The structure of a hexahistidine-tagged PurM has been solved by multiwavelength anomalous diffraction phasing techniques using protein containing 28 selenomethionines per asymmetric unit. The final model of PurM consists of two crystallographically independent dimers and four sulfates. The overall R factor at 2.5 A resolution is 19.2%, with an R(free) of 26.4%. The active site, identified in part by conserved residues, is proposed to be a long groove generated by the interaction of two monomers. A search of the sequence databases suggests that the ATP-binding sites between PurM and PurL may be structurally conserved. CONCLUSIONS: The first structure of a new class of ATP-binding enzyme, PurM, has been solved and a model for the active site has been proposed. The structure is unprecedented, with an extensive and unusual sheet-mediated intersubunit interaction defining the active-site grooves. Sequence searches suggest that two successive enzymes in the purine biosynthetic pathway, proposed to use similar chemistries, will have similar ATP-binding domains.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Structure of the PurM dimer. Ribbon diagram viewed down the twofold axis. Major structural features and the strands of the central b barrel, which form most of the dimer interface, are labeled. For subunit 1, the domain-A ribbon is highlighted in gold, the domain-B ribbon is highlighted in silver and the linker is shown in red. For subunit 2, the ribbon is highlighted in light blue.
 
  The above figure is reprinted by permission from Cell Press: Structure (1999, 7, 1155-1166) copyright 1999.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20693694 H.Xu (2010).
Enhancing MAD F(A) data for substructure determination.
  Acta Crystallogr D Biol Crystallogr, 66, 945-949.  
20633228 M.J.Gray, and J.C.Escalante-Semerena (2010).
A new pathway for the synthesis of α-ribazole-phosphate in Listeria innocua.
  Mol Microbiol, 77, 1429-1438.  
20631005 M.Welin, J.G.Grossmann, S.Flodin, T.Nyman, P.Stenmark, L.Trésaugues, T.Kotenyova, I.Johansson, P.Nordlund, and L.Lehtiö (2010).
Structural studies of tri-functional human GART.
  Nucleic Acids Res, 38, 7308-7319.
PDB codes: 2qk4 2v9y
19007868 A.J.Knox, C.Graham, J.Bleskan, G.Brodsky, and D.Patterson (2009).
Mutations in the Chinese hamster ovary cell GART gene of de novo purine synthesis.
  Gene, 429, 23-30.  
  18540050 E.Matsumoto, S.I.Sekine, R.Akasaka, Y.Otta, K.Katsura, M.Inoue, T.Kaminishi, T.Terada, M.Shirouzu, and S.Yokoyama (2008).
Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 453-458.
PDB code: 2zau
18065529 E.S.Rangarajan, A.Asinas, A.Proteau, C.Munger, J.Baardsnes, P.Iannuzzi, A.Matte, and M.Cygler (2008).
Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF.
  J Bacteriol, 190, 1447-1458.
PDB codes: 2i6r 2rb9
18219117 H.Xu, and C.M.Weeks (2008).
Rapid and automated substructure solution by Shake-and-Bake.
  Acta Crystallogr D Biol Crystallogr, 64, 172-177.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
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
17612488 S.Watanabe, R.Matsumi, T.Arai, H.Atomi, T.Imanaka, and K.Miki (2007).
Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling.
  Mol Cell, 27, 29-40.
PDB codes: 2z1c 2z1d 2z1e 2z1f
16544324 I.I.Mathews, S.S.Krishna, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, J.M.Canaves, H.J.Chiu, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, L.Jaroszewski, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, M.D.Miller, K.Moy, E.Nigoghossian, J.Paulsen, K.Quijano, R.Reyes, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, and I.A.Wilson (2006).
Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.
  Proteins, 63, 1106-1111.
PDB code: 1vk3
17154526 M.Morar, R.Anand, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2006).
Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily.
  Biochemistry, 45, 14880-14895.
PDB codes: 2hru 2hry 2hs0 2hs3 2hs4
15983421 H.Xu, C.M.Weeks, and H.A.Hauptman (2005).
Optimizing statistical Shake-and-Bake for Se-atom substructure determination.
  Acta Crystallogr D Biol Crystallogr, 61, 976-981.  
15558583 Y.Qi, and N.V.Grishin (2005).
Structural classification of thioredoxin-like fold proteins.
  Proteins, 58, 376-388.  
15502869 L.I.Leichert, and U.Jakob (2004).
Protein thiol modifications visualized in vivo.
  PLoS Biol, 2, e333.  
15291820 M.Blokesch, A.Paschos, A.Bauer, S.Reissmann, N.Drapal, and A.Böck (2004).
Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE.
  Eur J Biochem, 271, 3428-3436.  
14500881 K.Matsuda, T.Nishioka, K.Kinoshita, T.Kawabata, and N.Go (2003).
Finding evolutionary relations beyond superfamilies: fold-based superfamilies.
  Protein Sci, 12, 2239-2251.  
12586941 S.Reissmann, E.Hochleitner, H.Wang, A.Paschos, F.Lottspeich, R.S.Glass, and A.Böck (2003).
Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide ligands.
  Science, 299, 1067-1070.  
12377778 A.Paschos, A.Bauer, A.Zimmermann, E.Zehelein, and A.Böck (2002).
HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe] hydrogenase maturation.
  J Biol Chem, 277, 49945-49951.  
11244062 J.L.Zilles, T.J.Kappock, J.Stubbe, and D.M.Downs (2001).
Altered pathway routing in a class of Salmonella enterica serovar Typhimurium mutants defective in aminoimidazole ribonucleotide synthetase.
  J Bacteriol, 183, 2234-2240.  
11006535 S.E.Ealick (2000).
Advances in multiple wavelength anomalous diffraction crystallography.
  Curr Opin Chem Biol, 4, 495-499.  
11006546 T.J.Kappock, S.E.Ealick, and J.Stubbe (2000).
Modular evolution of the purine biosynthetic pathway.
  Curr Opin Chem Biol, 4, 567-572.  
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.