PDBsum entry 1l3c

Transferase, lyase

PDB id: 1l3c

Contents

Protein chains

186 a.a. *

Waters ×280

* Residue conservation analysis

PDB id:

1l3c

Name:

Transferase, lyase

Title:

Mt0146, the precorrin-6y methyltransferase (cbit) homolog from m. Thermoautotrophicum, c2 spacegroup with short cell

Structure:

Precorrin-6y methyltransferase/putative decarboxylase. Chain: a, b, c, d. Synonym: mt0146, cbit, mth146. Engineered: yes

Source:

Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Gene: mth146. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.31Å R-factor: 0.204 R-free: 0.254

Authors:

J.P.Keller,P.M.Smith,J.Benach,D.Christendat,G.Detitta,J.F.Hunt

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

Date:

26-Feb-02 Release date: 27-Nov-02

Protein chains

O26249  (CBIT_METTH) -  Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)

Seq: 192 a.a.

Struc: 186 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.196 - cobalt-precorrin-6B (C(15))-methyltransferase [decarboxylating].
• Reaction: Co-precorrin-6B + S-adenosyl-L-methionine = Co-precorrin-7 + S-adenosyl- L-homocysteine + CO2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

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.

ABSTRACT

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.