7XPR | pdb_00007xpr

Crystal structrue of SeMet-MtdL:GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.243 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

Structures of the NDP-pyranose mutase belonging to glycosyltransferase family 75 reveal residues important for Mn 2+ coordination and substrate binding.

Du, X.Chu, X.Liu, N.Jia, X.Peng, H.Xiao, Y.Liu, L.Yu, H.Li, F.He, C.

(2023) J Biological Chem 299: 102903-102903

  • DOI: https://doi.org/10.1016/j.jbc.2023.102903
  • Primary Citation Related Structures: 
    7XPR, 7XPS, 7XPT, 7XPU, 7XPV, 8HL8

  • PubMed Abstract: 

    Members of glycosyltransferase family 75 (GT75) not only reversibly catalyze the autoglycosylation of a conserved arginine residue with specific NDP-sugars but also exhibit NDP-pyranose mutase activity that reversibly converts specific NDP-pyranose to NDP-furanose. The latter activity provides valuable NDP-furanosyl donors for glycosyltransferases and requires a divalent cation as a cofactor instead of FAD used by UDP-D-galactopyranose mutase. However, details of the mechanism for NDP-pyranose mutase activity are not clear. Here we report the first crystal structures of GT75 family NDP-pyranose mutases. The novel structures of GT75 member MtdL in complex with Mn 2+ and GDP, GDP-D-glucopyranose, GDP-L-fucopyranose, GDP-L-fucofuranose, respectively, combined with site-directed mutagenesis studies, reveal key residues involved in Mn 2+ coordination, substrate binding, and catalytic reactions. We also provide a possible catalytic mechanism for this unique type of NDP-pyranose mutase. Taken together, our results highlight key elements of an enzyme family important for furanose biosynthesis.


  • Organizational Affiliation
    • Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui, China.

Macromolecule Content 

  • Total Structure Weight: 85.13 kDa 
  • Atom Count: 6,252 
  • Modeled Residue Count: 742 
  • Deposited Residue Count: 754 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transglycosylse
A, B
377Marinactinospora thermotoleransMutation(s): 0 
UniProt
Find proteins for G8HX37 (Marinactinospora thermotolerans)
Explore G8HX37 
Go to UniProtKB:  G8HX37
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8HX37
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.213α = 90
b = 97.483β = 97.32
c = 57.923γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXCDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary