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PDBsum entry 2fmn

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2fmn
Jmol
Contents
Protein chains
288 a.a. *
271 a.a. *
Ligands
FAD ×3
4HF ×3
Waters ×281
* Residue conservation analysis
PDB id:
2fmn
Name: Oxidoreductase
Title: Ala177val mutant of e. Coli methylenetetrahydrofolate reductase complex with ly309887
Structure: 5,10-methylenetetrahydrofolate reductase. Chain: a, b, c. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: metf. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.05Å     R-factor:   0.217     R-free:   0.250
Authors: R.Pejchal,E.Campbell,B.D.Guenther,B.W.Lennon,R.G.Matthews, M.L.Ludwig
Key ref:
R.Pejchal et al. (2006). Structural perturbations in the Ala --> Val polymorphism of methylenetetrahydrofolate reductase: how binding of folates may protect against inactivation. Biochemistry, 45, 4808-4818. PubMed id: 16605249 DOI: 10.1021/bi052294c
Date:
09-Jan-06     Release date:   25-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AEZ1  (METF_ECOLI) -  5,10-methylenetetrahydrofolate reductase
Seq:
Struc:
296 a.a.
288 a.a.*
Protein chain
Pfam   ArchSchema ?
P0AEZ1  (METF_ECOLI) -  5,10-methylenetetrahydrofolate reductase
Seq:
Struc:
296 a.a.
271 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C: E.C.1.5.1.20  - Methylenetetrahydrofolate reductase (NAD(P)H).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Coenzymes
      Reaction: 5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
5-methyltetrahydrofolate
+ NAD(P)(+)
= 5,10-methylenetetrahydrofolate
+ NAD(P)H
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     tetrahydrofolate interconversion   7 terms 
  Biochemical function     FAD binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi052294c Biochemistry 45:4808-4818 (2006)
PubMed id: 16605249  
 
 
Structural perturbations in the Ala --> Val polymorphism of methylenetetrahydrofolate reductase: how binding of folates may protect against inactivation.
R.Pejchal, E.Campbell, B.D.Guenther, B.W.Lennon, R.G.Matthews, M.L.Ludwig.
 
  ABSTRACT  
 
In human methylenetetrahydrofolate reductase (MTHFR) the Ala222Val (677C-->T) polymorphism encodes a heat-labile gene product that is associated with elevated levels of homocysteine and possibly with risk for cardiovascular disease. Generation of the equivalent Ala to Val mutation in Escherichia coli MTHFR, which is 30% identical to the catalytic domain of the human enzyme, creates a protein with enhanced thermolability. In both human and E. coli MTHFR, the A --> V mutation increases the rate of dissociation of FAD, and in both enzymes, loss of FAD is linked to changes in quaternary structure [Yamada, K., Chen, Z., Rozen, R., and Matthews, R. G. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 14853-14858; Guenther, B. D., Sheppard, C. A., Tran, P., Rozen, R., Matthews, R. G., and Ludwig, M. L. (1999) Nat. Struct. Biol. 6, 359-365]. Folates have been shown to protect both human and bacterial enzymes from loss of FAD. Despite its effect on affinity for FAD, the A --> V mutation is located at the bottom of the (betaalpha)(8) barrel of the catalytic domain in a position that does not contact the bound FAD prosthetic group. Here we report the structures of the Ala177Val mutant of E. coli MTHFR and of its complex with the 5,10-dideazafolate analogue, LY309887, and suggest mechanisms by which the mutation may perturb FAD binding. Helix alpha5, which immediately precedes the loop bearing the mutation, carries several residues that interact with FAD, including Asn168, Arg171, and Lys172. In the structures of the mutant enzyme this helix is displaced, perturbing protein-FAD interactions. In the complex with LY309887, the pterin-like ring of the analogue stacks against the si face of the flavin and is secured by hydrogen bonds to residues Gln183 and Asp120 that adjoin this face. The direct interactions of bound folate with the cofactor provide one mechanism for linkage between binding of FAD and folate binding that could account in part for the protective action of folates. Conformation changes induced by folate binding may also suppress dissociation of FAD.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20352077 E.Ciccimaro, and I.A.Blair (2010).
Stable-isotope dilution LC-MS for quantitative biomarker analysis.
  Bioanalysis, 2, 311-341.  
19610625 M.N.Lee, D.Takawira, A.P.Nikolova, D.P.Ballou, V.C.Furtado, N.L.Phung, B.R.Still, M.K.Thorstad, J.J.Tanner, and E.E.Trimmer (2009).
Functional role for the conformationally mobile phenylalanine 223 in the reaction of methylenetetrahydrofolate reductase from Escherichia coli.
  Biochemistry, 48, 7673-7685.
PDB codes: 3fst 3fsu
17896178 C.W.Cheng, J.C.Yu, C.S.Huang, J.C.Shieh, Y.P.Fu, H.W.Wang, P.E.Wu, and C.Y.Shen (2008).
Polymorphism of cytosolic serine hydroxymethyltransferase, estrogen and breast cancer risk among Chinese women in Taiwan.
  Breast Cancer Res Treat, 111, 145-155.  
17476281 V.M.Guillem, M.Collado, M.J.Terol, M.J.Calasanz, J.Esteve, M.Gonzalez, C.Sanzo, J.Nomdedeu, P.Bolufer, A.Lluch, and M.Tormo (2007).
Role of MTHFR (677, 1298) haplotype in the risk of developing secondary leukemia after treatment of breast cancer and hematological malignancies.
  Leukemia, 21, 1413-1422.  
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.