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PDBsum entry 2gca

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protein links
Ligase PDB id
2gca
Jmol
Contents
Protein chain
410 a.a. *
Waters ×201
* Residue conservation analysis
PDB id:
2gca
Name: Ligase
Title: Apo form of l. Casei fpgs
Structure: Folylpolyglutamate synthase. Chain: a. Synonym: folylpoly-gamma-glutamate synthetase, fpgs, tetrahydrofolate synthase, tetrahydrofolylpolyglutamate synthase. Engineered: yes
Source: Lactobacillus casei. Organism_taxid: 1582. Gene: fgs. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.174     R-free:   0.248
Authors: C.A.Smith,J.A.Cross,A.L.Bognar,X.Sun
Key ref:
C.A.Smith et al. (2006). Mutation of Gly51 to serine in the P-loop of Lactobacillus casei folylpolyglutamate synthetase abolishes activity by altering the conformation of two adjacent loops. Acta Crystallogr D Biol Crystallogr, 62, 548-558. PubMed id: 16627949 DOI: 10.1107/S0907444906009796
Date:
13-Mar-06     Release date:   27-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15925  (FOLC_LACCA) -  Folylpolyglutamate synthase
Seq:
Struc:
428 a.a.
410 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.17  - Tetrahydrofolate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Biosynthesis (late stages)
      Reaction: ATP + tetrahydropteroyl-(gamma-Glu)(n) + L-glutamate = ADP + phosphate + tetrahydropteroyl-(gamma-Glu)(n+1)
ATP
+ tetrahydropteroyl-(gamma-Glu)(n)
+ L-glutamate
= ADP
+ phosphate
+ tetrahydropteroyl-(gamma-Glu)(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     biosynthetic process   4 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1107/S0907444906009796 Acta Crystallogr D Biol Crystallogr 62:548-558 (2006)
PubMed id: 16627949  
 
 
Mutation of Gly51 to serine in the P-loop of Lactobacillus casei folylpolyglutamate synthetase abolishes activity by altering the conformation of two adjacent loops.
C.A.Smith, J.A.Cross, A.L.Bognar, X.Sun.
 
  ABSTRACT  
 
Based upon the three-dimensional structure of Lactobacillus casei folylpolyglutamate synthetase (FPGS), site-directed mutagenesis studies were performed on three residues associated with the ATPase site: Gly51, Ser52 and Ser73. Gly51 and Ser52 are at the end of the P-loop, which is involved in triphosphate binding. A G51S mutant enzyme and a G51S/S52T double-mutant enzyme were made in order to alter the FPGS P-loop to more closely resemble the sequences found in other ATPase and GTPase enzymes. Ser73 is on a neighboring loop (the Omega-loop) and precedes a proline residue found to be in a cis conformation. The carbonyl O atom of Ser73 is one of the protein ligands for the essential Mg(2+) ion involved in ATP binding and hydrolysis and the Omega-loop is involved in binding the folate substrate 5,10-methylenetetrahydrofolate. The serine residue was mutated to alanine and this is the only one of the three mutants which retains some FPGS activity. The structures of the G51S, G51S/S52T and S73A mutant proteins have been solved to high resolution, along with the structure of the apo wild-type FPGS. The P-loop in both the G51S and G51S/S52T mutant proteins remains unaltered, yet both structures show a large conformational rearrangement of the Omega-loop in which a cis-Pro residue has switched conformation to a trans-peptide. The structure of the Omega-loop is severely disrupted and as a consequence structural rearrangements are observed in the peptide linker joining the two domains of the enzyme. Magnesium binding in the active site is also disrupted by the presence of the serine side chain at position 51 and by the repositioning of the carbonyl O atom of Ser73 and a water molecule is bound in place of the Mg(2+) ion. The S73A mutant protein retains the cis-Pro configuration in the Omega-loop and the Mg(2+) site remains intact. The cis-Pro is also observed in the structure of the substrate-free form of FPGS (apoFPGS), maintained in the absence of Mg(2+) by a hydrogen-bonding network involving water molecules in the active site. It is only in the complete absence of water or Mg(2+) in the binding site that the cis-Pro switches to the trans conformation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Partial sequence alignment of the known prokaryotic and eukaryotic FPGS enzymes. Four regions have been chosen corresponding to the P-loop, the -loop, the loop following strand B4 (the Glu143 loop) and the linker connecting the N-terminal and C-terminal domains. Residues conserved across the prokaryotes and eukaryotes are shaded dark blue, while residues with a lower degree of conservation across both kingdoms are shaded in light blue. Residues conserved primarily in the prokaryotes are shaded light green and those predominantly observed in the eukaryotes are colored pink. The three residues mutated in this study are indicated with an asterisk. The numbering scheme relates to the Lactobacillus casei enzyme. The sequences used in this alignment are, in order, L. casei, Acinetobacter spp. ADP1, Aquifex aeolicus, Azotobacter vinelandii, Bacillus anthracis, B. subtilis, Campylobacter jejuni, Clostridium perfringens, Enterococcus faecalis, Escherichia coli, Geobacter metallireducens, Haemophilus influenzae, Helicobacter pylori, Leptospira interrogans, Mycobacterium tuberculosis, Neisseria meningitidis, Photorhabdus luminescens, Pseudomonas aeruginosa, Rickettsia prowazekii, Staphylococcus aureus, Streptococcus pyogenes, Streptomyces coelicolor, Thermotoga maritima, Thermus thermophilus, Trepanoma pallidum, Vibrio cholerae, Xylella fastidiosa, Anopheles gambiae (mosquito), Aspergillis fumigatus, Arabidopsis thaliana, Bos taurus (cow), Candida albicans, Caenorhabditis elegans, Canis familaris (dog), Cricetulus griseus (chinese hamster), Danio rerio (zebrafish), Dictyostelium discoideum (slime mold), Drosophila melanogaster, Homo sapiens, Leishmania major, Mus musculus (mouse), Neurospora crassa, Oryza sativa, Plasmodium falciparum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Trypanosoma brucei.
Figure 2.
Figure 2 Ribbon representation of the L. casei G51S FPGS mutant. The N-terminal domain is shown in blue, while the C-terminal domain is in red. The location of the P-loop (magenta) is indicated and the positions of the three mutations (G51S, S52T and S73A) are given. The -loop conformation seen in G51S is shown in cyan, overlaid with the loop conformation observed in the wild-type FPGS-MgATP structure, shown in black.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 548-558) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19706593 D.A.Gell, L.Feng, S.Zhou, P.D.Jeffrey, K.Bendak, A.Gow, M.J.Weiss, Y.Shi, and J.P.Mackay (2009).
A cis-proline in alpha-hemoglobin stabilizing protein directs the structural reorganization of alpha-hemoglobin.
  J Biol Chem, 284, 29462-29469.
PDB code: 3ia3
  17119116 U.Lim, S.S.Wang, P.Hartge, W.Cozen, L.E.Kelemen, S.Chanock, S.Davis, A.Blair, M.Schenk, N.Rothman, and Q.Lan (2007).
Gene-nutrient interactions among determinants of folate and one-carbon metabolism on the risk of non-Hodgkin lymphoma: NCI-SEER case-control study.
  Blood, 109, 3050-3059.  
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.