Crystal structure of unliganded Co2+2-HAI (pH 7.0)

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Crystal structures of complexes with cobalt-reconstituted human arginase I.

D'Antonio, E.L.Christianson, D.W.

(2011) Biochemistry 50: 8018-8027

  • DOI: https://doi.org/10.1021/bi201101t
  • Primary Citation of Related Structures:  
    3TF3, 3TH7, 3THE, 3THH, 3THJ

  • PubMed Abstract: 

    The binuclear manganese metalloenzyme human arginase I (HAI) is a potential protein drug for cancer chemotherapy, in that it is capable of depleting extracellular l-Arg levels in the microenvironment of tumor cells that require this nutrient to thrive. Substitution of the native Mn(2+)(2) cluster with a Co(2+)(2) cluster in the active site yields an enzyme with enhanced catalytic activity at physiological pH (∼7.4) that could serve as an improved protein drug for L-Arg depletion therapy [Stone, E. M., Glazer, E. S., Chantranupong, L., Cherukuri, P., Breece, R. M., Tierney, D. L., Curley, S. A., Iverson, B. L., and Georgiou, G. (2010) ACS Chem. Biol. 5, 333-342]. A different catalytic mechanism is proposed for Co(2+)(2)-HAI compared with that of Mn(2+)(2)-HAI, including an unusual Nε-Co(2+) coordination mode, to rationalize the lower K(M) value of L-Arg and the lower K(i) value of L-Orn. However, we now report that no unusual metal coordination modes are observed in the cobalt-reconstituted enzyme. The X-ray crystal structures of unliganded Co(2+)(2)-HAI determined at 2.10 Å resolution (pH 7.0) and 1.97 Å resolution (pH 8.5), as well as the structures of Co(2+)(2)-HAI complexed with the reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH, pH 7.0) and the catalytic product L-Orn (pH 7.0) determined at 1.85 and 1.50 Å resolution, respectively, are essentially identical to the corresponding structures of Mn(2+)(2)-HAI. Therefore, in the absence of significant structural differences between Co(2+)(2)-HAI and Mn(2+)(2)-HAI, we suggest that a higher concentration of metal-bridging hydroxide ion at physiological pH for Co(2+)(2)-HAI, a consequence of the lower pK(a) of a Co(2+)-bound water molecule compared with a Mn(2+)-bound water molecule, strengthens electrostatic interactions with cationic amino acids and accounts for enhanced affinity as reflected in the lower K(M) value of L-Arg and the lower K(i) value of L-Orn.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
322Homo sapiensMutation(s): 0 
Gene Names: ARG1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
GTEx:  ENSG00000118520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.282 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.406α = 90
b = 90.406β = 90
c = 69.741γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description