4QQU

Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The cobalamin-independent methionine synthase enzyme captured in a substrate-induced closed conformation.

Ubhi, D.K.Robertus, J.D.

(2015) J Mol Biol 427: 901-909

  • DOI: 10.1016/j.jmb.2014.12.014
  • Primary Citation of Related Structures:  
    4QQU

  • PubMed Abstract: 
  • The cobalamin-independent methionine synthase enzyme catalyzes a challenging reaction: the direct transfer of a methyl from 5-methyl-tetrahydrofolate-glutamate3 to the l-homocysteine thiol. The enzyme has a dual (βα)8 TIM barrel structure that binds, activates and brings the reactants into reaction proximity by conformational movements ...

    The cobalamin-independent methionine synthase enzyme catalyzes a challenging reaction: the direct transfer of a methyl from 5-methyl-tetrahydrofolate-glutamate3 to the l-homocysteine thiol. The enzyme has a dual (βα)8 TIM barrel structure that binds, activates and brings the reactants into reaction proximity by conformational movements. In the previously observed open structures, the substrates bind too far apart to react, but we have captured a ternary complex with both substrates bound in a closed form of the enzyme. The closing is described in terms of a hinge between the N- and C-terminal TIM barrels and a rearrangement of key loops within the C domain. The substrate specificity can now be rationalized and the structure reveals His707 as the acid that protonates the THF leaving group through a water molecule trapped in the closed active site. The substrates are correctly oriented for an in-line attack by l-homocysteine on the N(5)-methyl.


    Organizational Affiliation

    Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jrobertus@cm.utexas.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferaseA789Candida albicansMutation(s): 3 
Gene Names: CaO19.10083CaO19.2551MET6
EC: 2.1.1.14
UniProt
Find proteins for P82610 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore P82610 
Go to UniProtKB:  P82610
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
39S (Subject of Investigation/LOI)
Query on 39S

Download Ideal Coordinates CCD File 
F [auth A]N-[4-({[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-gamma-glutamyl-L-glutamic acid
C29 H37 N9 O12
RXWVHRYZTWZATH-XSLAGTTESA-N
 Ligand Interaction
HCS
Query on HCS

Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-4-MERCAPTO-BUTYRIC ACID
C4 H9 N O2 S
FFFHZYDWPBMWHY-VKHMYHEASA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.978α = 90
b = 99.102β = 90
c = 103.902γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Database references