PDBsum entry 2aeb

Hydrolase/hydrolase inhibitor

PDB id: 2aeb

Contents

Protein chain

314 a.a. *

Ligands

ABH ×2

Metals

_MN ×4

Waters ×384

* Residue conservation analysis

PDB id:

2aeb

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of human arginase i at 1.29 a resolution and exploration of inhibition in immune response.

Structure:

Arginase 1. Chain: a, b. Synonym: liver-type arginase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PDB file)

Resolution:

1.29Å R-factor: 0.165 R-free: 0.179

Authors:

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

Key ref:

L.Di Costanzo et al. (2005). Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response. Proc Natl Acad Sci U S A, 102, 13058-13063. PubMed id: 16141327 DOI: 10.1073/pnas.0504027102

Date:

21-Jul-05 Release date: 06-Sep-05

Protein chains

P05089  (ARGI1_HUMAN) -  Arginase-1 from Homo sapiens

Seq: 322 a.a.

Struc: 314 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.3.1 - arginase.
• Pathway: Urea Cycle and Arginine Biosynthesis
• Reaction: L-arginine + H2O = urea + L-ornithine

L-arginine + H2O = urea (Bound ligand (Het Group name = ABH) matches with 57.14% similarity) + L-ornithine

• Cofactor: Mn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.0504027102

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

PubMed id: 16141327

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

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

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, 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.

Selected figure(s)

Figure 2.
Fig. 2. Mechanism of human arginase I. New features suggested by the 1.29-Å resolution structure of the complex with ABH are the inner-sphere coordination of 2-NH[2] to in the tetrahedral intermediate, and the protonation of the amino leaving group of L-ornithine by the conformationally flexible imidazolium group of general acid H141. D128 may also donate a proton to L-ornithine before product release. In the final step of catalysis, the H141 imidazole may serve as a general base to abstract a proton from the metal-bridging water molecule (possibly through an intervening solvent molecule). For clarity, only the side chain guanidinium group of substrate L-arginine and the side chain amino group of product L-ornithine are indicated.

Figure 4.
Fig. 4. Arginase I-ABH complexes. Summary of average intermolecular interactions in the human arginase I-ABH complex (gray numbers) and the rat arginase I-ABH complex (orange numbers). Note that the higher resolution of the human arginase I-ABH structure allows for more accurate hydrogen bond distance measurements. Manganese coordination interactions are indicated by green dashed lines, and hydrogen bonds are indicated by black dashed lines. Several slightly shorter and stronger enzyme-inhibitor hydrogen bond interactions are observed in the human enzyme, consistent with its enhanced affinity for ABH (Table 2).

Figures were selected by an automated process.