5DML

Crystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli, Oxidized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.452 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the homocysteine methyltransferase MmuM from Escherichia coli.

Li, K.Li, G.Bradbury, L.M.Hanson, A.D.Bruner, S.D.

(2016) Biochem.J. 473: 277-284

  • DOI: 10.1042/BJ20150980
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homocysteine S-methyltransferases (HMTs, EC 2.1.1.0) catalyse the conversion of homocysteine to methionine using S-methylmethionine or S-adenosylmethionine as the methyl donor. HMTs play an important role in methionine biosynthesis and are widely dis ...

    Homocysteine S-methyltransferases (HMTs, EC 2.1.1.0) catalyse the conversion of homocysteine to methionine using S-methylmethionine or S-adenosylmethionine as the methyl donor. HMTs play an important role in methionine biosynthesis and are widely distributed among micro-organisms, plants and animals. Additionally, HMTs play a role in metabolite repair of S-adenosylmethionine by removing an inactive diastereomer from the pool. The mmuM gene product from Escherichia coli is an archetypal HMT family protein and contains a predicted zinc-binding motif in the enzyme active site. In the present study, we demonstrate X-ray structures for MmuM in oxidized, apo and metallated forms, representing the first such structures for any member of the HMT family. The structures reveal a metal/substrate-binding pocket distinct from those in related enzymes. The presented structure analysis and modelling of co-substrate interactions provide valuable insight into the function of MmuM in both methionine biosynthesis and cofactor repair.


    Organizational Affiliation

    Department of Chemistry, University of Florida, Gainesville, FL 32611, U.S.A.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homocysteine S-methyltransferase
A
310Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: mmuM (yagD)
EC: 2.1.1.10
Find proteins for Q47690 (Escherichia coli (strain K12))
Go to UniProtKB:  Q47690
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.452 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.453α = 90.00
b = 84.463β = 90.00
c = 85.821γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
ARPmodel building
PHENIXrefinement
Aimlessdata scaling
SHELXEmodel building
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of FloridaUnited States--
National Science Foundation (United States)United States1153413

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description