5HEC | pdb_00005hec

CgT structure in dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.204 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5HEC

This is version 1.5 of the entry. See complete history

Literature

New Helical Binding Domain Mediates a Glycosyltransferase Activity of a Bifunctional Protein.

Zhang, H.Zhou, M.Yang, T.Haslam, S.M.Dell, A.Wu, H.

(2016) J Biological Chem 291: 22106-22117

  • DOI: https://doi.org/10.1074/jbc.M116.731695
  • Primary Citation Related Structures: 
    5HEC

  • PubMed Abstract: 

    Serine-rich repeat glycoproteins (SRRPs) conserved in streptococci and staphylococci are important for bacterial colonization and pathogenesis. Fap1, a well studied SRRP is a major surface constituent of Streptococcus parasanguinis and is required for bacterial adhesion and biofilm formation. Biogenesis of Fap1 is a multistep process that involves both glycosylation and secretion. A series of glycosyltransferases catalyze sequential glycosylation of Fap1. We have identified a unique hybrid protein dGT1 (dual glycosyltransferase 1) that contains two distinct domains. N-terminal DUF1792 is a novel GT-D-type glycosyltransferase, transferring Glc residues to Glc-GlcNAc-modified Fap1. C-terminal dGT1 (CgT) is predicted to possess a typical GT-A-type glycosyltransferase, however, the activity remains unknown. In this study, we determine that CgT is a distinct glycosyltransferase, transferring GlcNAc residues to Glc-Glc-GlcNAc-modified Fap1. A 2.4-Å x-ray crystal structure reveals that CgT has a unique binding domain consisting of three α helices in addition to a typical GT-A-type glycosyltransferase domain. The helical domain is crucial for the oligomerization of CgT. Structural and biochemical studies revealed that the helix domain is required for the protein-protein interaction and crucial for the glycosyltransferase activity of CgT in vitro and in vivo As the helix domain presents a novel structural fold, we conclude that CgT represents a new member of GT-A-type glycosyltransferases.


  • Organizational Affiliation
    • From the Departments of Pediatric Dentistry and Microbiology, Schools of Dentistry and Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294 and.

Macromolecule Content 

  • Total Structure Weight: 68.59 kDa 
  • Atom Count: 4,745 
  • Modeled Residue Count: 552 
  • Deposited Residue Count: 592 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative glycosyltransferase (GalT1)
A, B
296Streptococcus parasanguinis FW213Mutation(s): 0 
Gene Names: galT1Spaf_1933
UniProt
Find proteins for I1ZPA1 (Streptococcus parasanguinis FW213)
Explore I1ZPA1 
Go to UniProtKB:  I1ZPA1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI1ZPA1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.204 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.044α = 90
b = 180.044β = 90
c = 62.985γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesR01DE017954

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary