6QAF image
Deposition Date 2018-12-19
Release Date 2019-12-11
Last Version Date 2024-01-24
Entry Detail
PDB ID:
6QAF
Keywords:
Title:
Crystal structure of human Arginase-1 at pH 9.0 in complex with CB-1158/INCB001158
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
1.61 Å
R-Value Free:
0.17
R-Value Work:
0.14
R-Value Observed:
0.14
Space Group:
P 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Arginase-1
Gene (Uniprot):ARG1
Chain IDs:A, B
Chain Length:342
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158.
J Struct Biol X 4 100014 100014 (2020)
PMID: 32647818 DOI: 10.1016/j.yjsbx.2019.100014

Abstact

Arginase-1 is a manganese-dependent metalloenzyme that catalyzes the hydrolysis of L-arginine into L-ornithine and urea. Arginase-1 is abundantly expressed by tumor-infiltrating myeloid cells that promote tumor immunosuppression, which is relieved by inhibition of Arginase-1. We have characterized the potencies of the Arginase-1 reference inhibitors (2S)-2-amino-6-boronohexanoic acid (ABH) and N ω-hydroxy-nor-L-arginine (nor-NOHA), and studied their pH-dependence and binding kinetics. To gain a better understanding of the structural changes underlying the high pH optimum of Arginase-1 and its pH-dependent inhibition, we determined the crystal structure of the human Arginase-1/ABH complex at pH 7.0 and 9.0. These structures revealed that at increased pH, the manganese cluster assumes a more symmetrical coordination structure, which presumably contributes to its increase in catalytic activity. Furthermore, we show that binding of ABH involves the presence of a sodium ion close to the manganese cluster. We also studied the investigational new drug CB-1158 (INCB001158). This inhibitor has a low-nanomolar potency at pH 7.4 and increases the thermal stability of Arginase-1 more than ABH and nor-NOHA. Moreover, CB-1158 displays slow association and dissociation kinetics at both pH 9.5 and 7.4, as indicated by surface plasmon resonance. The potent character of CB-1158 is presumably due to its increased rigidity compared to ABH as well as the formation of an additional hydrogen-bond network as observed by resolution of the Arginase-1/CB-1158 crystal structure.

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