1WVA

Crystal structure of human arginase I from twinned crystal

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of human arginase I at 1.29 A resolution and exploration of inhibition in the immune response

Di Costanzo, L., Sabio, G., Mora, A., Rodriguez, P.C., Ochoa, A.C., Centeno, F., Christianson, D.W.

(2005) Proc Natl Acad Sci U S A 102: 13058-13063

  • DOI: 10.1073/pnas.0504027102
  • Primary Citation of Related Structures:  
    2AEB, 1WVA

  • PubMed Abstract: 

    • Human arginase I is a potential target for therapeutic intervention in diseases linked to compromised l-arginine homeostasis. Here, we report high-affinity binding of the reaction coordinate analogue inhibitors 2(S)-amino-6-boronohexanoic acid (ABH, ...

    Human arginase I is a potential target for therapeutic intervention in diseases linked to compromised l-arginine homeostasis. Here, we report high-affinity binding of the reaction coordinate analogue inhibitors 2(S)-amino-6-boronohexanoic acid (ABH, Kd = 5 nM) and S-(2-boronoethyl)-l-cysteine (BEC, Kd = 270 nM) to human arginase I, and we report x-ray crystal structures of the respective enzyme-inhibitor complexes at 1.29- and 1.94-A resolution determined from crystals twinned by hemihedry. The ultrahigh-resolution structure of the human arginase I-ABH complex yields an unprecedented view of the binuclear manganese cluster and illuminates the structural basis for nanomolar affinity: bidentate inner-sphere boronate-manganese coordination interactions and fully saturated hydrogen bond networks with inhibitor alpha-amino and alpha-carboxylate groups. These interactions are therefore implicated in the stabilization of the transition state for l-arginine hydrolysis. Electron density maps also reveal that active-site residue H141 is protonated as the imidazolium cation. The location of H141 is such that it could function as a general acid to protonate the leaving amino group of l-ornithine during catalysis, and this is a revised mechanistic proposal for arginase. This work serves as a foundation for studying the structural and chemical biology of arginase I in the immune response, and we demonstrate the inhibition of arginase activity by ABH in human and murine myeloid cells.

    Related Citations: 
    • Human arginase II: crystal structure and physiological role in male and female sexual arousal
      Cama, E., Colleluori, D.M., Emig, F.A., Shin, H., Kim, S.W., Kim, N.N., Traish, A.M., Ash, D.E., Christianson, D.W.
      (2003) Biochemistry 42: 8445
    Organizational Affiliation: 

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginase 1A, B322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
NIH Common Fund Data Resources
PHAROS  P05089
GTEx  ENSG00000118520
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S2C
Query on S2C
Download CCD File 
A, B
S-2-(BORONOETHYL)-L-CYSTEINE
C5 H13 B N O5 S
XLVRIIJULVQAMP-BYPYZUCNSA-N		 Ligand Interaction
MN
Query on MN
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S2CKd:  270   nM  Binding MOAD
S2CKd :  270   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.602α = 90
b = 90.602β = 90
c = 69.311γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance