5DML

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    5DMN, 5DMM, 5DML

  • 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 distributed among micro-organisms, plants and animals ...

    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. bruner@ufl.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Homocysteine S-methyltransferaseA310Escherichia coli K-12Mutation(s): 0 
Gene Names: mmuMyagDb0261JW0253
EC: 2.1.1.10
Find proteins for Q47690 (Escherichia coli (strain K12))
Explore Q47690 
Go to UniProtKB:  Q47690
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.453α = 90
b = 84.463β = 90
c = 85.821γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
ARPmodel building
MOLREPphasing
SHELXDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2016-02-03
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Refinement description
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence