PDBsum entry 1f38

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protein Protein-protein interface(s) links
Lyase PDB id
Protein chains
186 a.a. *
Waters ×180
* Residue conservation analysis
PDB id:
Name: Lyase
Title: X-ray crystallographic structure of precorrin 8w decarboxylase, the product of gene mt0146 in the methanobacterium thermoautotrophicum genome
Structure: Precorrin-8w decarboxylase. Chain: a, b, c, d. Engineered: yes
Source: Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Gene: mt0146. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: genomic DNA
Biol. unit: Tetramer (from PQS)
2.40Å     R-factor:   0.236     R-free:   0.291
Authors: J.P.Keller,P.M.Smith,J.F.Hunt,Northeast Structural Genomics Consortium (Nesg)
Key ref:
J.P.Keller et al. (2002). The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure, 10, 1475-1487. PubMed id: 12429089 DOI: 10.1016/S0969-2126(02)00876-6
31-May-00     Release date:   10-Jun-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O26249  (CBIT_METTH) -  Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)
192 a.a.
186 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Cobalt-precorrin-6B (C(15))-methyltransferase (decarboxylating).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cobalt-precorrin-6B + S-adenosyl-L-methionine = cobalt-precorrin-7 + S-adenosyl-L-homocysteine + CO2
+ S-adenosyl-L-methionine
= cobalt-precorrin-7
+ S-adenosyl-L-homocysteine
+ CO(2)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methylation   4 terms 
  Biochemical function     transferase activity     3 terms  


DOI no: 10.1016/S0969-2126(02)00876-6 Structure 10:1475-1487 (2002)
PubMed id: 12429089  
The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase.
J.P.Keller, P.M.Smith, J.Benach, D.Christendat, G.T.deTitta, J.F.Hunt.
The CbiT and CbiE enzymes participate in the biosynthesis of vitamin B12. They are fused together in some organisms to form a protein called CobL, which catalyzes two methylations and one decarboxylation on a precorrin intermediate. Because CbiE has sequence homology to canonical precorrin methyltransferases, CbiT was hypothesized to catalyze the decarboxylation. We herein present the crystal structure of MT0146, the CbiT homolog from Methanobacterium thermoautotrophicum. The protein shows structural similarity to Rossmann-like S-adenosyl-methionine-dependent methyltransferases, and our 1.9 A cocrystal structure shows that it binds S-adenosyl-methionine in standard geometry near a binding pocket that could accommodate a precorrin substrate. Therefore, MT0146/CbiT probably functions as a precorrin methyltransferase and represents the first enzyme identified with this activity that does not have the canonical precorrin methyltransferase fold.
  Selected figure(s)  
Figure 4.
Figure 4. Structure of the Methyltransferase Active Site(A) Stereo ribbon diagram showing the F[o] - F[c] difference density (magenta) observed in the active site of the AdoHcy-bound MT0146/CbiT crystal form with molecular replacement phases calculated from the apo model. The electron density was contoured at 3.5 s. The coordinates of the AdoHcy molecule shown in ball and stick representation came from the structure of the COMT homolog [12] on the basis of the structural alignment of its methyltransferase fold to that of MT0146/CbiT by the program DALI.(B) Stereo pair showing the binding contacts to the AdoHcy molecule in the refined MT0146/CbiT complex structure.
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 1475-1487) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944207 M.D.Miller, L.Aravind, C.Bakolitsa, C.L.Rife, D.Carlton, P.Abdubek, T.Astakhova, H.L.Axelrod, H.J.Chiu, T.Clayton, M.C.Deller, L.Duan, J.Feuerhelm, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1167-1173.
PDB code: 3l5o
19543979 D.Bandyopadhyay, J.Huan, J.Prins, J.Snoeyink, W.Wang, and A.Tropsha (2009).
Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development.
  J Comput Aided Mol Des, 23, 773-784.  
18818720 R.Mazumder, and S.Vasudevan (2008).
Structure-guided comparative analysis of proteins: principles, tools, and applications for predicting function.
  PLoS Comput Biol, 4, e1000151.  
17154423 N.Mirkovic, Z.Li, A.Parnassa, and D.Murray (2007).
Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization.
  Proteins, 66, 766-777.  
18073103 W.A.Hendrickson (2007).
Impact of structures from the protein structure initiative.
  Structure, 15, 1528-1529.  
16936030 C.A.Roessner, and A.I.Scott (2006).
Fine-tuning our knowledge of the anaerobic route to cobalamin (vitamin B12).
  J Bacteriol, 188, 7331-7334.  
16225687 P.Z.Kozbial, and A.R.Mushegian (2005).
Natural history of S-adenosylmethionine-binding proteins.
  BMC Struct Biol, 5, 19.  
16243268 Y.Ofran, M.Punta, R.Schneider, and B.Rost (2005).
Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.
  Drug Discov Today, 10, 1475-1482.  
15036155 A.F.Yakunin, A.A.Yee, A.Savchenko, A.M.Edwards, and C.H.Arrowsmith (2004).
Structural proteomics: a tool for genome annotation.
  Curr Opin Chem Biol, 8, 42-48.  
14739239 M.Roovers, J.Wouters, J.M.Bujnicki, C.Tricot, V.Stalon, H.Grosjean, and L.Droogmans (2004).
A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.
  Nucleic Acids Res, 32, 465-476.  
12547423 C.Zhang, and S.H.Kim (2003).
Overview of structural genomics: from structure to function.
  Curr Opin Chem Biol, 7, 28-32.  
12826405 H.L.Schubert, R.M.Blumenthal, and X.Cheng (2003).
Many paths to methyltransfer: a chronicle of convergence.
  Trends Biochem Sci, 28, 329-335.  
12831893 K.Kinoshita, and H.Nakamura (2003).
Protein informatics towards function identification.
  Curr Opin Struct Biol, 13, 396-400.  
14595395 M.E.Stroupe, H.K.Leech, D.S.Daniels, M.J.Warren, and E.D.Getzoff (2003).
CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis.
  Nat Struct Biol, 10, 1064-1073.
PDB codes: 1pjq 1pjs 1pjt
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.