8IKR

Crystal structure of DpaA

Summary for 8IKR

• Entry DOI: 10.2210/pdb8ikr/pdb
• Descriptor: YkuD domain-containing protein (1 entity in total)
• Functional Keywords: peptidoglycan, hydrolase, amidase, yukd
• Biological source: Escherichia coli 908519
• Total number of polymer chains: 2
• Total formula weight: 54337.61

Authors

Wang, H.-J.,Hsieh, K.-Y.,Lee, S.-H.,Chang, C.-I. (deposition date: 2023-03-01, release date: 2023-10-11, Last modification date: 2023-11-29)

Primary citation

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.
Structural basis for the hydrolytic activity of the transpeptidase-like protein DpaA to detach Braun's lipoprotein from peptidoglycan.
Mbio, 14:e0137923-e0137923, 2023

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.

PubMed: 37830798
DOI: 10.1128/mbio.01379-23

Experimental method

X-RAY DIFFRACTION (2.9 Å)