5GIQ

Xaa-Pro peptidase from Deinococcus radiodurans, Zinc bound

Summary for 5GIQ

• Entry DOI: 10.2210/pdb5giq/pdb
• Related: 5CDL 5CDV 5GIU
• Descriptor: Proline dipeptidase, PHOSPHATE ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: xaa-pro peptidase, m24b fold, proline-specific, hydrolase
• Biological source: Deinococcus radiodurans R1
• Total number of polymer chains: 1
• Total formula weight: 37372.53

Authors

Are, V.N.,Singh, R.,Kumar, A.,Ghosh, B.,Jamdar, S.N.,Makde, R.D. (deposition date: 2016-06-24, release date: 2017-06-28, 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 (1.8 Å)