Crystal structure of Treponema pallidum protein Tp0624

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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The Structure of Treponema pallidum Tp0624 Reveals a Modular Assembly of Divergently Functionalized and Previously Uncharacterized Domains.

Parker, M.L.Houston, S.Wetherell, C.Cameron, C.E.Boulanger, M.J.

(2016) PLoS One 11: e0166274-e0166274

  • DOI: https://doi.org/10.1371/journal.pone.0166274
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Treponema pallidum subspecies pallidum is the causative agent of syphilis, a chronic, multistage, systemic infection that remains a major global health concern. The molecular mechanisms underlying T. pallidum pathogenesis are incompletely understood, partially due to the phylogenetic divergence of T. pallidum. One aspect of T. pallidum that differentiates it from conventional Gram-negative bacteria, and is believed to play an important role in pathogenesis, is its unusual cell envelope ultrastructure; in particular, the T. pallidum peptidoglycan layer is chemically distinct, thinner and more distal to the outer membrane. Established functional roles for peptidoglycan include contributing to the structural integrity of the cell envelope and stabilization of the flagellar motor complex, which are typically mediated by the OmpA domain-containing family of proteins. To gain insight into the molecular mechanisms that govern peptidoglycan binding and cell envelope biogenesis in T. pallidum we report here the structural characterization of the putative OmpA-like domain-containing protein, Tp0624. Analysis of the 1.70 Å resolution Tp0624 crystal structure reveals a multi-modular architecture comprised of three distinct domains including a C-terminal divergent OmpA-like domain, which we show is unable to bind the conventional peptidoglycan component diaminopimelic acid, and a previously uncharacterized tandem domain unit. Intriguingly, bioinformatic analysis indicates that the three domains together are found in all orthologs from pathogenic treponemes, but are not observed together in genera outside Treponema. These findings provide the first structural insight into a multi-modular treponemal protein containing an OmpA-like domain and its potential role in peptidoglycan coordination and stabilization of the T. pallidum cell envelope.

  • Organizational Affiliation

    Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OOP family OmpA-OmpF porinA [auth B],
B [auth A]
421Treponema pallidum subsp. pallidum str. NicholsMutation(s): 0 
Gene Names: TP_0624TPANIC_0624
Find proteins for O83632 (Treponema pallidum (strain Nichols))
Explore O83632 
Go to UniProtKB:  O83632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO83632
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B],
I [auth A],
J [auth A],
K [auth A]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
D [auth B]
E [auth B]
F [auth B]
G [auth B]
H [auth B]
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
L [auth A],
M [auth A],
N [auth A]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.02α = 90
b = 103.5β = 90
c = 140.68γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references