Crystal structure of RlpA SPOR domain from Pseudomonas aeruginosa in complex with nuded glycan obtained by co-crystallization

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Structural basis of denuded glycan recognition by SPOR domains in bacterial cell division.

Alcorlo, M.Dik, D.A.De Benedetti, S.Mahasenan, K.V.Lee, M.Dominguez-Gil, T.Hesek, D.Lastochkin, E.Lopez, D.Boggess, B.Mobashery, S.Hermoso, J.A.

(2019) Nat Commun 10: 5567-5567

  • DOI: https://doi.org/10.1038/s41467-019-13354-4
  • Primary Citation of Related Structures:  
    6I05, 6I09, 6I0A, 6I0N

  • PubMed Abstract: 

    SPOR domains are widely present in bacterial proteins that recognize cell-wall peptidoglycan strands stripped of the peptide stems. This type of peptidoglycan is enriched in the septal ring as a product of catalysis by cell-wall amidases that participate in the separation of daughter cells during cell division. Here, we document binding of synthetic denuded glycan ligands to the SPOR domain of the lytic transglycosylase RlpA from Pseudomonas aeruginosa (SPOR-RlpA) by mass spectrometry and structural analyses, and demonstrate that indeed the presence of peptide stems in the peptidoglycan abrogates binding. The crystal structures of the SPOR domain, in the apo state and in complex with different synthetic glycan ligands, provide insights into the molecular basis for recognition and delineate a conserved pattern in other SPOR domains. The biological and structural observations presented here are followed up by molecular-dynamics simulations and by exploration of the effect on binding of distinct peptidoglycan modifications.

  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolytic peptidoglycan transglycosylase RlpA77Pseudomonas aeruginosaMutation(s): 0 
Gene Names: rlpAPAMH19_1027
EC: 4.2.2
Find proteins for Q9X6V6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9X6V6 
Go to UniProtKB:  Q9X6V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6V6
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside
Glycosylation Resources
GlyTouCan:  G12322WX
GlyCosmos:  G12322WX
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.567α = 90
b = 68.219β = 90
c = 39.097γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-59389-P and BFU2017-90030-P to JAH

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary