1LFW

Crystal structure of pepV

Summary for 1LFW

• Entry DOI: 10.2210/pdb1lfw/pdb
• Descriptor: pepV, ZINC ION, 3-[(1-AMINO-2-CARBOXY-ETHYL)-HYDROXY-PHOSPHINOYL]-2-METHYL-PROPIONIC ACID, ... (4 entities in total)
• Functional Keywords: hydrolase, dipeptidase
• Biological source: Lactobacillus delbrueckii
• Cellular location: Cytoplasm (Probable): P45494
• Total number of polymer chains: 1
• Total formula weight: 52415.09

Authors

Jozic, D.,Bourenkow, G.,Bartunik, H.,Scholze, H.,Dive, V.,Henrich, B.,Huber, R.,Bode, W.,Maskos, K. (deposition date: 2002-04-12, release date: 2002-10-23, Last modification date: 2024-03-13)

Primary citation

Jozic, D.,Bourenkow, G.,Bartunik, H.,Scholze, H.,Dive, V.,Henrich, B.,Huber, R.,Bode, W.,Maskos, K.
Crystal Structure of the Dinuclear Zinc Aminopeptidase PepV from Lactobacillus delbrueckii Unravels Its Preference for Dipeptides
Structure, 10:1097-1106, 2002

PubMed Abstract: PepV from Lactobacillus delbrueckii, a dinuclear zinc peptidase, has been characterized as an unspecific amino dipeptidase. The crystal structure of PepV in complex with the phosphinic inhibitor AspPsi[PO(2)CH(2)]AlaOH, a dipeptide substrate mimetic, reveals a "catalytic domain" and a "lid domain," which together form an internal active site cavity that traps the inhibitor. The catalytic domain is topologically similar to catalytic domains from amino- and carboxypeptidases. However, the lid domain is unique among the related enzymes. In contrast to the other related exopeptidases, PepV recognizes and fixes the dipeptide backbone, while the side chains are not specifically probed and can vary, rendering it a nonspecific dipeptidase. The cocrystallized inhibitor illustrates the two roles of the two catalytic zinc ions, namely stabilization of the tetrahedral intermediate and activation of the catalytic water molecule.

PubMed: 12176387
DOI: 10.1016/S0969-2126(02)00805-5

Experimental method

X-RAY DIFFRACTION (1.8 Å)