Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83362.86 
• Atom Count: 5836 
• Residue Count: 738 
• Unique protein chains: 1

1ITQ

HUMAN RENAL DIPEPTIDASE

• DOI: 10.2210/pdb1ITQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris


• Deposited: 2002-02-02 Released: 2002-08-28 
• Deposition Author(s): Nitanai, Y., Satow, Y., Adachi, H., Tsujimoto, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.258 
• R-Value Work: 0.181 

Literature

Crystal Structure of Human Renal Dipeptidase Involved in beta-Lactam Hydrolysis

Nitanai, Y., Satow, Y., Adachi, H., Tsujimoto, M.

(2002) J.Mol.Biol. 321: 177-184

• PubMed: 12144777 
• Primary Citation of Related Structures:  
  1ITU


• PubMed Abstract: 
  

Human renal dipeptidase is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. The crystal structures of the saccharide-trimmed enzyme are determined as unliganded and inhibitor-liganded forms. They are informative for designing new antibiotics that are not hydrolyzed by this enzyme. The active site in each of the (alpha/beta)(8) barrel subunits of the homodimeric molecule is composed of binuclear zinc ions bridged by the Glu125 side-chain located at the bottom of the barrel, and it faces toward the microvillar membrane of a kidney tubule. A dipeptidyl moiety of the therapeutically used cilastatin inhibitor is fully accommodated in the active-site pocket, which is small enough for precise recognition of dipeptide substrates. The barrel and active-site architectures utilizing catalytic metal ions exhibit unexpected similarities to those of the murine adenosine deaminase and the catalytic domain of the bacterial urease.

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Related Citations: 

• Crystallization and preliminary X-ray investigation of a glycoprotein, human renal dipeptidase
  Nitanai, Y.,Satow, Y.,Adachi, H.,Tsujimoto, M.
  (1996) J.CRYST.GROWTH 168: 280




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Organizational Affiliation: 

Faculty of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RENAL DIPEPTIDASE	A, B	369	Homo sapiens	Gene Names: DPEP1 (MDP, RDP) EC: 3.4.13.19
Find proteins for P16444 (Homo sapiens) Go to Gene View: DPEP1 Go to UniProtKB:  P16444

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.258 
• R-Value Work: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 81.948	α = 90.00
b = 81.213	β = 96.73
c = 57.164	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-02-02 
• Released Date: 2002-08-28 
• Deposition Author(s): Nitanai, Y., Satow, Y., Adachi, H., Tsujimoto, M.

Revision History 

• Version 1.0: 2002-08-28
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance