PDBsum entry 3bus

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protein ligands Protein-protein interface(s) links
Transferase PDB id
Protein chains
251 a.a. *
SAH ×2
Waters ×6
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of rebm
Structure: Methyltransferase. Chain: a, b. Synonym: rebm. Engineered: yes
Source: Lechevalieria aerocolonigenes. Organism_taxid: 68170. Gene: rbmf, rebm. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.65Å     R-factor:   0.217     R-free:   0.260
Authors: J.G.Mccoy,S.Singh,C.A.Bingman,J.S.Thorson,G.N.Phillips Jr.
Key ref:
S.Singh et al. (2008). Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM. J Biol Chem, 283, 22628-22636. PubMed id: 18502766 DOI: 10.1074/jbc.M800503200
03-Jan-08     Release date:   25-Mar-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8KZ94  (REBMT_NOCAE) -  Demethylrebeccamycin-D-glucose O-methyltransferase
283 a.a.
251 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Demethylrebeccamycin-D-glucose O-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4'-demethylrebeccamycin + S-adenosyl-L-methionine = rebeccamycin + S-adenosyl-L-homocysteine
+ S-adenosyl-L-methionine
= rebeccamycin
Bound ligand (Het Group name = SAH)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     transferase activity     2 terms  


    Added reference    
DOI no: 10.1074/jbc.M800503200 J Biol Chem 283:22628-22636 (2008)
PubMed id: 18502766  
Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM.
S.Singh, J.G.McCoy, C.Zhang, C.A.Bingman, G.N.Phillips, J.S.Thorson.
The 2.65-angstroms crystal structure of the rebeccamycin 4'-O-methyltransferase RebM in complex with S-adenosyl-l-homocysteine revealed RebM to adopt a typical S-adenosylmethionine-binding fold of small molecule O-methyltransferases (O-MTases) and display a weak dimerization domain unique to MTases. Using this structure as a basis, the RebM substrate binding model implicated a predominance of nonspecific hydrophobic interactions consistent with the reported ability of RebM to methylate a wide range of indolocarbazole surrogates. This model also illuminated the three putative RebM catalytic residues (His140/141 and Asp166) subsequently found to be highly conserved among sequence-related natural product O-MTases from GC-rich bacteria. Interrogation of these residues via site-directed mutagenesis in RebM demonstrated His140 and Asp166 to be most important for catalysis. This study reveals RebM to be a member of the general acid/base-dependent O-MTases and, as the first crystal structure for a sugar O-MTase, may also present a template toward the future engineering of natural product MTases for combinatorial applications.
  Selected figure(s)  
Figure 1.
A, naturally occurring indolocarbazoles staurosporine (1), K252a (2), rebeccamycin (3), and AT2433A1 (4). B, the putative biosynthetic pathways for 1, 3, and 4. The reaction catalyzed by RebM is highlighted in the box.
Figure 3.
Comparison of the overall topologies of structural homologs. A, structural overlay of RebM from L. aerocolonigenes (Protein Data Bank code 3BUS) colored pink and sarcosine dimethylglycine methyltransferase from Galdieria sulfuraria (Protein Data Bank code 2O57) colored green (root mean square (RSM) deviation between the structures is 1.8 Å). B, structural overlay of RebM from L. aerocolonigenes (Protein Data Bank code 3BUS) colored pink and mycolic acid synthase Hma (Mmaa4) from Mycobacterium tuberculosis (Protein Data Bank code 2FK8) colored blue (root mean square (RSM) deviation between the structures is 2.0 Å). AdoHcy (SAH) is in stick model and colored yellow. The molecular graphics program PyMOL was used in generating these graphics. C, sequence alignment of RebM from L. aerocolonigenes (Protein Data Bank code 3BUS), sarcosine dimethylglycine methyltransferase (GNMT, glycine N-methyltransferase) from G. sulfuraria (Protein Data Bank code 2O57), mycolic acid synthase Hma (Mmaa4) (Protein Data Bank code 2FK8) from M. tuberculosis, mycolic acid cyclopropane synthase (Cmaa1) (Protein Data Bank code 1KPH) from M. tuberculosis, and carminomycin 4-O-methyltransferase (DnrK) (Protein Data Bank code 1TW3) from Streptomyces peucetius. In this alignment, the predicted secondary structure is illustrated above the sequence. Helices and sheets are colored red and green, respectively, wherein yellow-colored helices α8, α9, and α10 indicate incomplete sequence. Loops involved in cofactor binding are labeled (L1–L3), and sequence of blue color designates the AdoMet binding core domain (β1–β7 and α1–α3, α5, and α7). Highly or moderately conserved residues are colored red and orange, respectively, with putative catalytic residues (based upon RebM mutagenesis) colored green.
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 22628-22636) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19857499 I.Gómez García, C.E.Stevenson, I.Usón, C.L.Freel Meyers, C.T.Walsh, and D.M.Lawson (2010).
The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily.
  J Mol Biol, 395, 390-407.
PDB code: 2wk1
20876132 J.H.Lee, B.Bae, M.Kuemin, B.T.Circello, W.W.Metcalf, S.K.Nair, and W.A.van der Donk (2010).
Characterization and structure of DhpI, a phosphonate O-methyltransferase involved in dehydrophos biosynthesis.
  Proc Natl Acad Sci U S A, 107, 17557-17562.
PDB codes: 3ou2 3ou6 3ou7
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