5CNX

Crystal structure of Xaa-Pro aminopeptidase from Escherichia coli K12

Summary for 5CNX

• Entry DOI: 10.2210/pdb5cnx/pdb
• Descriptor: Aminopeptidase YpdF, ZINC ION, CACODYLATE ION, ... (6 entities in total)
• Functional Keywords: xaa-pro aminopeptidase, pepq, prolidase, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 3
• Total formula weight: 119780.43

Authors

Kumar, A.,Are, V.,Ghosh, B.,Jamdar, S.,Makde, R.D. (deposition date: 2015-07-18, release date: 2016-07-20, Last modification date: 2023-11-08)

Primary citation

Are, V.N.,Kumar, A.,Goyal, V.D.,Gotad, S.S.,Ghosh, B.,Gadre, R.,Jamdar, S.N.,Makde, R.D.
Structures and activities of widely conserved small prokaryotic aminopeptidases-P clarify classification of M24B peptidases
Proteins, 2018

PubMed Abstract: M24B peptidases cleaving Xaa-Pro bond in dipeptides are prolidases whereas those cleaving this bond in longer peptides are aminopeptidases-P. Bacteria have small aminopeptidases-P (36-39 kDa), which are diverged from canonical aminopeptidase-P of Escherichia coli (50 kDa). Structure-function studies of small aminopeptidases-P are lacking. We report crystal structures of small aminopeptidases-P from E. coli and Deinococcus radiodurans, and report substrate-specificities of these proteins and their ortholog from Mycobacterium tuberculosis. These are aminopeptidases-P, structurally close to small prolidases except for absence of dipeptide-selectivity loop. We noticed absence of this loop and conserved arginine in canonical archaeal prolidase (Maher et al., Biochemistry. 43, 2004, 2771-2783) and questioned its classification. Our enzymatic assays show that this enzyme is an aminopeptidase-P. Further, our mutagenesis studies illuminate importance of DXRY sequence motif in bacterial small aminopeptidases-P and suggest common evolutionary origin with human XPNPEP1/XPNPEP2. Our analyses reveal sequence/structural features distinguishing small aminopeptidases-P from other M24B peptidases.

PubMed: 30536999
DOI: 10.1002/prot.25641

Experimental method

X-RAY DIFFRACTION (2.6 Å)