6EJC | pdb_00006ejc

Human Xylosyltransferase 1 in complex with peptide QEEEGSGVGQGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.273 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1.

Briggs, D.C.Hohenester, E.

(2018) Structure 26: 801-809.e3

  • DOI: https://doi.org/10.1016/j.str.2018.03.014
  • Primary Citation Related Structures: 
    6EJ7, 6EJ8, 6EJ9, 6EJA, 6EJB, 6EJC, 6EJD, 6EJE, 6FOA

  • PubMed Abstract: 

    Proteoglycans (PGs) are essential components of the animal extracellular matrix and are required for cell adhesion, migration, signaling, and immune function. PGs are composed of a core protein and long glycosaminoglycan (GAG) chains, which often specify PG function. GAG biosynthesis is initiated by peptide O-xylosyltransferases, which transfer xylose onto selected serine residues in the core proteins. We have determined crystal structures of human xylosyltransferase 1 (XT1) in complex with the sugar donor, UDP-xylose, and various acceptor peptides. The structures reveal unique active-site features that, in conjunction with functional experiments, explain the substrate specificity of XT1. A constriction within the peptide binding cleft requires the acceptor serine to be followed by glycine or alanine. The remainder of the cleft can accommodate a wide variety of sequences, but with a general preference for acidic residues. These findings provide a framework for understanding the selectivity of GAG attachment.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College London, London SW7 2AZ, UK. Electronic address: david.briggs@crick.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 87.37 kDa 
  • Atom Count: 5,669 
  • Modeled Residue Count: 710 
  • Deposited Residue Count: 763 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Xylosyltransferase 1751Homo sapiensMutation(s): 0 
Gene Names: XYLT1XT1
EC: 2.4.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q86Y38 (Homo sapiens)
Explore Q86Y38 
Go to UniProtKB:  Q86Y38
PHAROS:  Q86Y38
GTEx:  ENSG00000103489 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86Y38
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein AMBP12Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for P02760 (Homo sapiens)
Explore P02760 
Go to UniProtKB:  P02760
PHAROS:  P02760
GTEx:  ENSG00000106927 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02760
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.273 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.626α = 90
b = 86.898β = 90
c = 152.389γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101748/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary