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PDBsum entry 1xra

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protein ligands metals links
Methyltransferase PDB id
1xra
Jmol
Contents
Protein chain
377 a.a. *
Ligands
PO4 ×2
Metals
__K ×2
_MG ×2
* Residue conservation analysis
PDB id:
1xra
Name: Methyltransferase
Title: Crystal structure of s-adenosylmethionine synthetase
Structure: S-adenosylmethionine synthetase. Chain: a. Synonym: mat, atp:l-methionine s-adenosyltransferase. Ec: 2.5.1.6
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
3.00Å     R-factor:   0.189     R-free:   0.260
Authors: F.Takusagawa,S.Kamitori,S.Misaki,G.D.Markham
Key ref: F.Takusagawa et al. (1996). Crystal structure of S-adenosylmethionine synthetase. J Biol Chem, 271, 136-147. PubMed id: 8550549
Date:
26-Oct-95     Release date:   08-Mar-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A817  (METK_ECOLI) -  S-adenosylmethionine synthase
Seq:
Struc:
384 a.a.
377 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.5.1.6  - Methionine adenosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Methionine Adenosyltransferase
      Reaction: ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L- methionine
ATP
+ L-methionine
+ H(2)O
=
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
+ diphosphate
+ S-adenosyl-L- methionine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     one-carbon metabolic process   2 terms 
  Biochemical function     nucleotide binding     9 terms  

 

 
    reference    
 
 
J Biol Chem 271:136-147 (1996)
PubMed id: 8550549  
 
 
Crystal structure of S-adenosylmethionine synthetase.
F.Takusagawa, S.Kamitori, S.Misaki, G.D.Markham.
 
  ABSTRACT  
 
The structure of S-adenosylmethionine synthetase (MAT, ATP:L-methionine S-adenosyltransferase, EC 2.5.1.6.) from Escherichia coli has been determined at 3.0 A resolution by multiple isomorphous replacement using a uranium derivative and the selenomethionine form of the enzyme (SeMAT). The SeMAT data (9 selenomethionine residues out of 383 amino acid residues) have been found to have a sufficient phasing power to determine the structure of the 42,000 molecular weight protein by combining them with the other heavy atom derivative data (multiple isomorphous replacement). The enzyme consists of four identical subunits; two subunits form a spherical tight dimer, and pairs of these dimers form a peanut-shaped tetrameric enzyme. Each pair dimer has two active sites which are located between the subunits. Each subunit consists of three domains that are related to each other by pseudo-3-fold symmetry. The essential divalent (Mg2+/Co2+) and monovalent (K+) metal ions and one of the product, Pi ions, were found in the active site from three separate structures.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19348969 F.Garrido, C.Alfonso, J.C.Taylor, G.D.Markham, and M.A.Pajares (2009).
Subunit association as the stabilizing determinant for archaeal methionine adenosyltransferases.
  Biochim Biophys Acta, 1794, 1082-1090.  
18953685 G.D.Markham, and M.A.Pajares (2009).
Structure-function relationships in methionine adenosyltransferases.
  Cell Mol Life Sci, 66, 636-648.  
18621724 A.M.van Roon, N.M.Loening, E.Obayashi, J.C.Yang, A.J.Newman, H.Hernández, K.Nagai, and D.Neuhaus (2008).
Solution structure of the U2 snRNP protein Rds3p reveals a knotted zinc-finger motif.
  Proc Natl Acad Sci U S A, 105, 9621-9626.
PDB code: 2k0a
18317700 Y.An, J.Ji, W.Wu, R.Huang, Y.Wei, and Z.Xiu (2008).
Random mutagenesis and recombination of sam1 gene by integrating error-prone PCR with staggered extension process.
  Biotechnol Lett, 30, 1227-1232.  
18163700 M.L.Mansfield (2007).
Efficient knot group identification as a tool for studying entanglements of polymers.
  J Chem Phys, 127, 244901.  
17915037 P.Ho, K.F.Kong, Y.H.Chan, J.S.Tsang, and J.T.Wong (2007).
An unusual S-adenosylmethionine synthetase gene from dinoflagellate is methylated.
  BMC Mol Biol, 8, 87.  
16672621 B.A.McDaniel, F.J.Grundy, V.P.Kurlekar, J.Tomsic, and T.M.Henkin (2006).
Identification of a mutation in the Bacillus subtilis S-adenosylmethionine synthetase gene that results in derepression of S-box gene expression.
  J Bacteriol, 188, 3674-3681.  
16299822 M.R.Duff, and C.V.Kumar (2005).
Site-selective photocleavage of proteins by uranyl ions.
  Angew Chem Int Ed Engl, 45, 137-139.  
15189891 I.Iloro, R.Chehín, F.M.Goñi, M.A.Pajares, and J.L.Arrondo (2004).
Methionine adenosyltransferase alpha-helix structure unfolds at lower temperatures than beta-sheet: a 2D-IR study.
  Biophys J, 86, 3951-3958.  
15206944 Y.Pérez-Pertejo, R.M.Reguera, C.García-Estrada, R.Balaña-Fouce, and D.Ordóñez (2004).
Mutational analysis of methionine adenosyltransferase from Leishmania donovani.
  Eur J Biochem, 271, 2791-2798.  
12809568 B.J.Berger, and M.H.Knodel (2003).
Characterisation of methionine adenosyltransferase from Mycobacterium smegmatis and M. tuberculosis.
  BMC Microbiol, 3, 12.  
12951252 J.Slapeta, F.Stejskal, and J.S.Keithly (2003).
Characterization of S-adenosylmethionine synthetase in Cryptosporidium parvum (Apicomplexa).
  FEMS Microbiol Lett, 225, 271-277.  
12056895 G.D.Markham, P.O.Norrby, and C.W.Bock (2002).
S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group.
  Biochemistry, 41, 7636-7646.  
11266562 J.Mrázek, D.Bhaya, A.R.Grossman, and S.Karlin (2001).
Highly expressed and alien genes of the Synechocystis genome.
  Nucleic Acids Res, 29, 1590-1601.  
11489855 S.Karlin, J.Mrázek, A.Campbell, and D.Kaiser (2001).
Characterizations of highly expressed genes of four fast-growing bacteria.
  J Bacteriol, 183, 5025-5040.  
10674710 J.Y.Chou (2000).
Molecular genetics of hepatic methionine adenosyltransferase deficiency.
  Pharmacol Ther, 85, 1-9.  
10601859 M.L.Martínez-Chantar, and M.A.Pajares (2000).
Assignment of a single disulfide bridge in rat liver methionine adenosyltransferase.
  Eur J Biochem, 267, 132-137.  
10757994 M.S.McQueney, K.S.Anderson, and G.D.Markham (2000).
Energetics of S-adenosylmethionine synthetase catalysis.
  Biochemistry, 39, 4443-4454.  
10029549 C.Schalk-Hihi, and G.D.Markham (1999).
The conformations of a substrate and a product bound to the active site of S-adenosylmethionine synthetase.
  Biochemistry, 38, 2542-2550.  
10467129 H.S.Radeke, C.A.Digits, R.L.Casaubon, and M.L.Snapper (1999).
Interactions of (-)-ilimaquinone with methylation enzymes: implications for vesicular-mediated secretion.
  Chem Biol, 6, 639-647.  
9753435 R.S.Reczkowski, J.C.Taylor, and G.D.Markham (1998).
The active-site arginine of S-adenosylmethionine synthetase orients the reaction intermediate.
  Biochemistry, 37, 13499-13506.  
9482646 S.Hazelwood, I.Bernardini, V.Shotelersuk, A.Tangerman, J.Guo, H.Mudd, and W.A.Gahl (1998).
Normal brain myelination in a patient homozygous for a mutation that encodes a severely truncated methionine adenosyltransferase I/III.
  Am J Med Genet, 75, 395-400.  
  9409150 D.Thomas, and Y.Surdin-Kerjan (1997).
Metabolism of sulfur amino acids in Saccharomyces cerevisiae.
  Microbiol Mol Biol Rev, 61, 503-532.  
9175157 J.M.Mato, L.Alvarez, P.Ortiz, and M.A.Pajares (1997).
S-adenosylmethionine synthesis: molecular mechanisms and clinical implications.
  Pharmacol Ther, 73, 265-280.  
9202427 J.Mingorance, L.Alvarez, M.A.Pajares, and J.M.Mato (1997).
Recombinant rat liver S-adenosyl-L-methionine synthetase tetramers and dimers are in equilibrium.
  Int J Biochem Cell Biol, 29, 485-491.  
  9042912 M.E.Chamberlin, T.Ubagai, S.H.Mudd, H.L.Levy, and J.Y.Chou (1997).
Dominant inheritance of isolated hypermethioninemia is associated with a mutation in the human methionine adenosyltransferase 1A gene.
  Am J Hum Genet, 60, 540-546.  
9164450 M.L.Mansfield (1997).
Fit to be tied.
  Nat Struct Biol, 4, 166-167.  
8611562 F.Takusagawa, S.Kamitori, and G.D.Markham (1996).
Structure and function of S-adenosylmethionine synthetase: crystal structures of S-adenosylmethionine synthetase with ADP, BrADP, and PPi at 28 angstroms resolution.
  Biochemistry, 35, 2586-2596.
PDB codes: 1mxa 1mxb 1mxc
  8978034 J.L.Barra, M.R.Mautino, and A.L.Rosa (1996).
A dominant negative effect of eth-1r, a mutant allele of the Neurospora crassa S-adenosylmethionine synthetase-encoding gene conferring resistance to the methionine toxic analogue ethionine.
  Genetics, 144, 1455-1462.  
8939751 M.M.Dixon, S.Huang, R.G.Matthews, and M.Ludwig (1996).
The structure of the C-terminal domain of methionine synthase: presenting S-adenosylmethionine for reductive methylation of B12.
  Structure, 4, 1263-1275.
PDB code: 1msk
8672457 S.Rhee, K.D.Parris, S.A.Ahmed, E.W.Miles, and D.R.Davies (1996).
Exchange of K+ or Cs+ for Na+ induces local and long-range changes in the three-dimensional structure of the tryptophan synthase alpha2beta2 complex.
  Biochemistry, 35, 4211-4221.
PDB codes: 1ttp 1ttq 1ubs
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.