4Z8I | pdb_00004z8i

Crystal structure of Branchiostoma belcheri tsingtauense peptidoglycan recognition protein 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.201 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4Z8I

This is version 1.3 of the entry. See complete history

Literature

Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain

Wang, W.J.Cheng, W.Luo, M.Yan, Q.Yu, H.M.Li, Q.Cao, D.D.Huang, S.Xu, A.Mariuzza, R.A.Chen, Y.Zhou, C.Z.

(2015) PLoS One 10: e0140953-e0140953

  • DOI: https://doi.org/10.1371/journal.pone.0140953
  • Primary Citation Related Structures: 
    4Z8I, 4ZXM

  • PubMed Abstract: 

    Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 Å crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecule Content 

  • Total Structure Weight: 25.52 kDa 
  • Atom Count: 1,766 
  • Modeled Residue Count: 224 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
peptidoglycan recognition protein 3236Branchiostoma belcheri tsingtauenseMutation(s): 0 
EC: 3.5.1.28
UniProt
Find proteins for A0A0R4I979 (Branchiostoma belcheri tsingtauense)
Explore A0A0R4I979 
Go to UniProtKB:  A0A0R4I979
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4I979
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.201 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.206α = 90
b = 77.206β = 90
c = 82.607γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2013CB835300
Ministry of Science and Technology of ChinaChina2014CB910100
Hefei Science Center of CASChina2015SRG-HSC045
Hefei Science Center of CASChina2015SRG-HSC046

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-14
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary