1UQT | pdb_00001uqt

Trehalose-6-phosphate from E. coli bound with UDP-2-fluoro glucose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.251 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1UQT

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

The donor subsite of trehalose-6-phosphate synthase: binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 A resolution.

Gibson, R.P.Tarling, C.A.Roberts, S.Withers, S.G.Davies, G.J.

(2004) J Biological Chem 279: 1950-1955

  • DOI: https://doi.org/10.1074/jbc.M307643200
  • Primary Citation Related Structures: 
    1UQT, 1UQU

  • PubMed Abstract: 

    Trehalose is an unusual non-reducing disaccharide that plays a variety of biological roles, from food storage to cellular protection from environmental stresses such as desiccation, pressure, heat-shock, extreme cold, and oxygen radicals. It is also an integral component of the cell-wall glycolipids of mycobacteria. The primary enzymatic route to trehalose first involves the transfer of glucose from a UDP-glucose donor to glucose-6-phosphate to form alpha,alpha-1,1 trehalose-6-phosphate. This reaction, in which the configurations of two glycosidic bonds are set simultaneously, is catalyzed by the glycosyltransferase trehalose-6-phosphate synthase (OtsA), which acts with retention of the anomeric configuration of the UDP-sugar donor. The classification of activated sugar-dependent glycosyltransferases into approximately 70 distinct families based upon amino acid sequence similarities places OtsA in glycosyltransferase family 20 (see afmb.cnrs-mrs.fr/CAZY/). The recent 2.4 A structure of Escherichia coli OtsA revealed a two-domain enzyme with catalysis occurring at the interface of the twin beta/alpha/beta domains. Here we present the 2.0 A structures of the E. coli OtsA in complex with either UDP-Glc or the non-transferable analogue UDP-2-deoxy-2-fluoroglucose. Both complexes unveil the donor subsite interactions, confirming a strong similarity to glycogen phosphorylases, and reveal substantial conformational differences to the previously reported complex with UDP and glucose 6-phosphate. Both the relative orientation of the two domains and substantial (up to 10 A) movements of an N-terminal loop (residues 9-22) characterize the more open "relaxed" conformation of the binary UDP-sugar complexes reported here.


  • Organizational Affiliation
    • Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 110.63 kDa 
  • Atom Count: 7,411 
  • Modeled Residue Count: 902 
  • Deposited Residue Count: 964 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE
A, B
482Escherichia coliMutation(s): 0 
EC: 2.4.1.15
UniProt
Find proteins for P31677 (Escherichia coli (strain K12))
Explore P31677 
Go to UniProtKB:  P31677
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31677
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U2F

Query on U2F



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
C15 H23 F N2 O16 P2
NGTCPFGWXMBZEP-NQQHDEILSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.251 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.919α = 90
b = 101.521β = 90
c = 118.207γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-28
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2018-05-02
    Changes: Data collection
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description