2Y4K | pdb_00002y4k

MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH MG-GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.225 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2Y4K

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Substrate and Metal Ion Promiscuity in Mannosylglycerate Synthase.

Nielsen, M.M.Suits, M.D.L.Yang, M.Barry, C.S.Martinez-Fleites, C.Tailford, L.E.Flint, J.E.Dumon, C.Davis, B.G.Gilbert, H.J.Davies, G.J.

(2011) J Biological Chem 286: 15155

  • DOI: https://doi.org/10.1074/jbc.M110.199844
  • Primary Citation Related Structures: 
    2Y4J, 2Y4K, 2Y4L, 2Y4M

  • PubMed Abstract: 

    The enzymatic transfer of the sugar mannose from activated sugar donors is central to the synthesis of a wide range of biologically significant polysaccharides and glycoconjugates. In addition to their importance in cellular biology, mannosyltransferases also provide model systems with which to study catalytic mechanisms of glycosyl transfer. Mannosylglycerate synthase (MGS) catalyzes the synthesis of α-mannosyl-D-glycerate using GDP-mannose as the preferred donor species, a reaction that occurs with a net retention of anomeric configuration. Past work has shown that the Rhodothermus marinus MGS, classified as a GT78 glycosyltransferase, displays a GT-A fold and performs catalysis in a metal ion-dependent manner. MGS shows very unusual metal ion dependences with Mg(2+) and Ca(2+) and, to a lesser extent, Mn(2+), Ni(2+), and Co(2+), thus facilitating catalysis. Here, we probe these dependences through kinetic and calorimetric analyses of wild-type and site-directed variants of the enzyme. Mutation of residues that interact with the guanine base of GDP are correlated with a higher k(cat) value, whereas substitution of His-217, a key component of the metal coordination site, results in a change in metal specificity to Mn(2+). Structural analyses of MGS complexes not only provide insight into metal coordination but also how lactate can function as an alternative acceptor to glycerate. These studies highlight the role of flexible loops in the active center and the subsequent coordination of the divalent metal ion as key factors in MGS catalysis and metal ion dependence. Furthermore, Tyr-220, located on a flexible loop whose conformation is likely influenced by metal binding, also plays a critical role in substrate binding.


  • Organizational Affiliation
    • Institute for Cell and Molecular Biosciences, Newcastle University, Medical School, Newcastle upon Tyne NE2 4HH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 90.61 kDa 
  • Atom Count: 6,449 
  • Modeled Residue Count: 758 
  • Deposited Residue Count: 764 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MANNOSYLGLYCERATE SYNTHASE
A, B
382Rhodothermus marinus DSM 4252Mutation(s): 2 
EC: 2.4.1.217
UniProt
Find proteins for D0MI02 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Explore D0MI02 
Go to UniProtKB:  D0MI02
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0MI02
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
L [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
FMT

Query on FMT



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
M [auth B]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
M [auth B],
N [auth B],
O [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.646α = 90
b = 149.646β = 90
c = 154.112γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description