4ICQ

Structural basis for substrate recognition and reaction mechanism of bacterial aminopeptidase peps

Summary for 4ICQ

• Entry DOI: 10.2210/pdb4icq/pdb
• Related: 4ICR 4ICS
• Descriptor: Aminopeptidase PepS, ZINC ION (3 entities in total)
• Functional Keywords: peps, aminopeptidase, clan mq, hydrolase
• Biological source: Streptococcus pneumoniae
• Total number of polymer chains: 2
• Total formula weight: 90839.32

Authors

Ta, M.H.,Kim, K.K.,Lee, S. (deposition date: 2012-12-11, release date: 2013-10-23, Last modification date: 2024-02-28)

Primary citation

Ta, H.M.,Bae, S.,Han, S.,Song, J.,Ahn, T.K.,Hohng, S.,Lee, S.,Kim, K.K.
Structure-based elucidation of the regulatory mechanism for aminopeptidase activity.
Acta Crystallogr.,Sect.D, 69:1738-1747, 2013

PubMed Abstract: The specificity of proteases for the residues in and length of substrates is key to understanding their regulatory mechanism, but little is known about length selectivity. Crystal structure analyses of the bacterial aminopeptidase PepS, combined with functional and single-molecule FRET assays, have elucidated a molecular basis for length selectivity. PepS exists in open and closed conformations. Substrates can access the binding hole in the open conformation, but catalytic competency is only achieved in the closed conformation by formation of the S1 binding pocket and proximal movement of Glu343, a general base, to the cleavage site. Hence, peptides longer than the depth of the binding hole block the transition from the open to the closed conformation, and thus length selection is a prerequisite for catalytic activation. A triple-sieve interlock mechanism is proposed featuring the coupling of length selectivity with residue specificity and active-site positioning.

PubMed: 23999297
DOI: 10.1107/S0907444913012651

Experimental method

X-RAY DIFFRACTION (2.25 Å)