1ZPE | pdb_00001zpe

Arginase I covalently modified with butylamine at Q19C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1ZPE

This is version 1.5 of the entry. See complete history

Literature

Probing the role of the hyper-reactive histidine residue of arginase.

Colleluori, D.M.Reczkowski, R.S.Emig, F.A.Cama, E.Cox, J.D.Scolnick, L.R.Compher, K.Jude, K.Han, S.Viola, R.E.Christianson, D.W.Ash, D.E.

(2005) Arch Biochem Biophys 444: 15-26

  • DOI: https://doi.org/10.1016/j.abb.2005.09.009
  • Primary Citation Related Structures: 
    1TA1, 1TBH, 1TBJ, 1TBL, 1ZPE, 1ZPG

  • PubMed Abstract: 

    Rat liver arginase (arginase I) is potently inactivated by diethyl pyrocarbonate, with a second-order rate constant of 113M(-1)s(-1) for the inactivation process at pH 7.0, 25 degrees C. Partial protection from inactivation is provided by the product of the reaction, l-ornithine, while nearly complete protection is afforded by the inhibitor pair, l-ornithine and borate. The role of H141 has been probed by mutagenesis, chemical modulation, and X-ray diffraction. The hyper-reactivity of H141 towards diethyl pyrocarbonate can be explained by its proximity to E277. A proton shuttling role for H141 is supported by its conformational mobility observed among the known arginase structures. H141 is proposed to serve as an acid/base catalyst, deprotonating the metal-bridging water molecule to generate the metal-bridging hydroxide nucleophile, and by protonating the amino group of the product to facilitate its departure.


  • Organizational Affiliation
    • Department of Biochemistry, Temple University School of Medicine, Philadelphia, PA 19140, USA.

Macromolecule Content 

  • Total Structure Weight: 102.08 kDa 
  • Atom Count: 7,666 
  • Modeled Residue Count: 942 
  • Deposited Residue Count: 942 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase 1
A, B, C
314Rattus norvegicusMutation(s): 5 
Gene Names: Arg1
EC: 3.5.3.1
UniProt
Find proteins for P07824 (Rattus norvegicus)
Explore P07824 
Go to UniProtKB:  P07824
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07824
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.078α = 90
b = 88.078β = 90
c = 106.34γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection, Derived calculations