1LFW

Crystal structure of pepV

• PDB DOI: https://doi.org/10.2210/pdb1LFW/pdb

• Classification: HYDROLASE
• Organism(s): Lactobacillus delbrueckii subsp. lactis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-04-12 Released: 2002-10-23 
• Deposition Author(s): Jozic, D., Bourenkow, G., Bartunik, H., Scholze, H., Dive, V., Henrich, B., Huber, R., Bode, W., Maskos, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.174 

Literature

Crystal Structure of the Dinuclear Zinc Aminopeptidase PepV from Lactobacillus delbrueckii Unravels Its Preference for Dipeptides

Jozic, D., Bourenkow, G., Bartunik, H., Scholze, H., Dive, V., Henrich, B., Huber, R., Bode, W., Maskos, K.

(2002) Structure 10: 1097-1106

• PubMed: 12176387 
• DOI: https://doi.org/10.1016/s0969-2126(02)00805-5
• Primary Citation of Related Structures:  
  1LFW


• 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.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.42 kDa 
• Atom Count: 4,238 
• Modelled Residue Count: 468 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pepV	A	470	Lactobacillus delbrueckii subsp. lactis	Mutation(s): 0  EC: 3.4.13.3 (PDB Primary Data), 3.4.13 (UniProt)
UniProt
Find proteins for P45494 (Lactobacillus delbrueckii subsp. lactis) Explore P45494  Go to UniProtKB:  P45494

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AEP	D [auth A]	3-[(1-AMINO-2-CARBOXY-ETHYL)-HYDROXY-PHOSPHINOYL]-2-METHYL-PROPIONIC ACID C7 H14 N O6 P NJOTXUMMTTYQMQ-RFZPGFLSSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.151	α = 90
b = 77.025	β = 90
c = 89.955	γ = 90

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-23 
Deposition Author(s): Jozic, D., Bourenkow, G., Bartunik, H., Scholze, H., Dive, V., Henrich, B., Huber, R., Bode, W., Maskos, K.

Revision History  

• Version 1.0: 2002-10-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-03-19
  Changes: Source and taxonomy
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations