8IKR | pdb_00008ikr

Crystal structure of DpaA

• PDB DOI: https://doi.org/10.2210/pdb8IKR/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli 908519
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-01 Released: 2023-10-11 
• Deposition Author(s): Wang, H.-J., Hsieh, K.-Y., Lee, S.-H., Chang, C.-I.
• Funding Organization(s): National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.274 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.215 (Depositor) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the hydrolytic activity of the transpeptidase-like protein DpaA to detach Braun's lipoprotein from peptidoglycan.

Wang, H.J., Hernandez-Rocamora, V.M., Kuo, C.I., Hsieh, K.Y., Lee, S.H., Ho, M.R., Tu, Z., Vollmer, W., Chang, C.I.

(2023) mBio 14: e0137923-e0137923

• PubMed: 37830798 
• DOI: https://doi.org/10.1128/mbio.01379-23
• Primary Citation Related Structures: 
  8IKR


• PubMed Abstract: 
  

  Cross-linking reaction of Braun's lipoprotein (Lpp) to peptidoglycan (PG) is catalyzed by some members of the YkuD family of transpeptidases. However, the exact opposite reaction of cleaving the Lpp-PG cross-link is performed by DpaA, which is also a YkuD-like protein. In this work, we determined the crystal structure of DpaA to provide the molecular rationale for the ability of the transpeptidase-like protein to cleave, rather than form, the Lpp-PG linkage. Our findings also revealed the structural features that distinguish the different functional types of the YkuD family enzymes from one another.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.
Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University , Newcastle upon Tyne, United Kingdom.
Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland, Australia.
College of Life Science, Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.34 kDa 
• Atom Count: 3,033 
• Modeled Residue Count: 371 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YkuD domain-containing protein	A, B	236	Escherichia coli 908519	Mutation(s): 0  Gene Names: HMPREF1604_05013 EC: 3.4
UniProt
Find proteins for P0AA99 (Escherichia coli (strain K12)) Explore P0AA99  Go to UniProtKB:  P0AA99

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.274 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.215 (Depositor) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.876	α = 90
b = 86.876	β = 90
c = 150.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Wang, H.-J., Hsieh, K.-Y., Lee, S.-H., Chang, C.-I.

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Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	NSTC108-2320-B-001-011-MY3

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Database references