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PDBsum entry 1u3f

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
1u3f
Jmol
Contents
Protein chains
164 a.a. *
Ligands
PO4 ×2
ADP ×2
Metals
_MG ×2
Waters ×245
* Residue conservation analysis
PDB id:
1u3f
Name: Ligase
Title: Structural and functional characterization of a 5,10- methenyltetrahydrofolate synthetase from mycoplasma pneumoniae (gi: 13508087)
Structure: 5,10-methenyltetrahydrofolate synthetase. Chain: a, b. Synonym: h91_orf164, hypothetical protein mg245 homolog. Engineered: yes
Source: Mycoplasma pneumoniae. Organism_taxid: 2104. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.50Å     R-factor:   0.223     R-free:   0.268
Authors: S.Chen,A.F.Yakunin,M.Proudfoot,R.Kim,S.-H.Kim,Berkeley Structural Genomics Center (Bsgc)
Key ref:
S.Chen et al. (2004). Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution. Proteins, 56, 839-843. PubMed id: 15281135 DOI: 10.1002/prot.20214
Date:
21-Jul-04     Release date:   07-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P75430  (MTHFS_MYCPN) -  5-formyltetrahydrofolate cyclo-ligase
Seq:
Struc:
164 a.a.
164 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.3.2  - 5-formyltetrahydrofolate cyclo-ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Coenzymes
      Reaction: ATP + 5-formyltetrahydrofolate = ADP + phosphate + 5,10- methenyltetrahydrofolate
ATP
+ 5-formyltetrahydrofolate
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
+ 5,10- methenyltetrahydrofolate
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     metabolic process   1 term 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.20214 Proteins 56:839-843 (2004)
PubMed id: 15281135  
 
 
Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution.
S.Chen, D.H.Shin, R.Pufan, R.Kim, S.H.Kim.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Sequence comparison of M. pneumoniae MTHFS to its homologs. Conserved residues are shaded, and the highly conserved region is marked. Eight homologs were selected for sequence comparison: MP_MTHFS (gi13508087; M. pneumoniae); MG_MTHFS (gi12045099; Mycoplasma genitalium); AA_MTHFS (gi15606807; Aquifex aeolicus); GS_MTHFS (gi39996238; Geobacter sulfurreducens PCA); CH__MTHFS (gi23137790; Cytophaga hutchinsonii); GP_MTHFS (gi9971879; uncultured marine gamma proteobacterium EBAC31A08); HM_MTHFS (gi5453746; Homo sapiens); MM_MTHFS (gi18093092; Mus musculus); RN_MTHFS (gi34865439; Rattus norvegicus).
Figure 2.
Figure 2. (a) Backbone representation of M. pneumoniae MTHFS monomer structure. The residues in the highly conserved region are labeled, and their side chains are shown in black. (b) Electrostatic potential surface of M. pneumoniae MTHFS (red, negatively charged surface; blue, positively charged surface; white, uncharged surface). (c) Backbone superimposition of M. pneumoniae MTHFS (in red) and its closest structural homolog D-ribose-5-phosphate isomerase (Rpia; PDB ID 1O8B; in blue). The bound sulfate ion in M. pneumoniae MTHFS and the bound -D-arabinofuranise-5 -phosphate in 1O8B are shown in a ball-and-stick model. The side chains of the active site residues that interact with sulfate and -D-arabinofuranise-5 -phosphate are shown in red and blue, respectively. (d) Electrostatic potential surface of D-ribose-5-phosphate isomerase (red, negatively charged surface; blue, positively charged surface; white, uncharged surface).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 839-843) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18473156 A.N.Hancock, R.S.Coleman, R.T.Johnson, C.A.Sarisky, and T.W.Johann (2008).
Investigations of the roles of arginine 115 and lysine 120 in the active site of 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae.
  Protein J, 27, 303-308.  
  17329806 C.Meier, L.G.Carter, G.Winter, R.J.Owens, D.I.Stuart, and R.M.Esnouf (2007).
Structure of 5-formyltetrahydrofolate cyclo-ligase from Bacillus anthracis (BA4489).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 168-172.
PDB code: 2jcb
16365037 M.S.Field, D.M.Szebenyi, and P.J.Stover (2006).
Regulation of de novo purine biosynthesis by methenyltetrahydrofolate synthetase in neuroblastoma.
  J Biol Chem, 281, 4215-4221.  
16104022 S.Chen, A.F.Yakunin, M.Proudfoot, R.Kim, and S.H.Kim (2005).
Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087).
  Proteins, 61, 433-443.  
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.