7AU2

Cryo-EM structure of human exostosin-like 3 (EXTL3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis.

Wilson, L.F.L.Dendooven, T.Hardwick, S.W.Echevarria-Poza, A.Tryfona, T.Krogh, K.B.R.M.Chirgadze, D.Y.Luisi, B.F.Logan, D.T.Mani, K.Dupree, P.

(2022) Nat Commun 13: 3314-3314

  • DOI: https://doi.org/10.1038/s41467-022-31048-2
  • Primary Citation of Related Structures:  
    7AU2, 7AUA

  • PubMed Abstract: 

    Heparan sulfate is a highly modified O-linked glycan that performs diverse physiological roles in animal tissues. Though quickly modified, it is initially synthesised as a polysaccharide of alternating β-D-glucuronosyl and N-acetyl-α-D-glucosaminyl residues by exostosins. These enzymes generally possess two glycosyltransferase domains (GT47 and GT64)-each thought to add one type of monosaccharide unit to the backbone. Although previous structures of murine exostosin-like 2 (EXTL2) provide insight into the GT64 domain, the rest of the bi-domain architecture is yet to be characterised; hence, how the two domains co-operate is unknown. Here, we report the structure of human exostosin-like 3 (EXTL3) in apo and UDP-bound forms. We explain the ineffectiveness of EXTL3's GT47 domain to transfer β-D-glucuronosyl units, and we observe that, in general, the bi-domain architecture would preclude a processive mechanism of backbone extension. We therefore propose that heparan sulfate backbone polymerisation occurs by a simple dissociative mechanism.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exostosin-like 3
A, B
890Homo sapiensMutation(s): 0 
Gene Names: EXTL3EXTL1LEXTR1KIAA0519
EC: 2.4.1.223
UniProt & NIH Common Fund Data Resources
Find proteins for O43909 (Homo sapiens)
Explore O43909 
Go to UniProtKB:  O43909
PHAROS:  O43909
GTEx:  ENSG00000012232 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43909
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, F
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2
RECONSTRUCTIONRELION2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--
Wellcome TrustUnited Kingdom200873/Z/16/Z
Swedish Research CouncilSweden2014-03402
Swedish Research CouncilSweden2016-04855
CancerfondenSweden180710
Engineering and Physical Sciences Research CouncilUnited Kingdom--
University of CambridgeUnited Kingdom--
OpenPlantUnited KingdomBB/L014130/1

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references