PDBsum entry 6lrh

Hydrolase

PDB id: 6lrh

Contents

Protein chains

675 a.a.

Ligands

ARG ×2

Waters ×44

PDB id:

6lrh

Name:

Hydrolase

Title:

Crystal structure of the binary complex of agre c264a mutant with l- arginine

Structure:

Alr4995 protein. Chain: a, b. Synonym: arginine-guanidine removing enzyme. Engineered: yes. Mutation: yes

Source:

Nostoc sp. (Strain pcc 7120 / sag 25.82 / utex 2576). Organism_taxid: 103690. Strain: pcc 7120 / sag 25.82 / utex 2576. Gene: alr4995. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.71Å R-factor: 0.195 R-free: 0.245

Authors:

H.Lee,S.Rhee

Key ref:

H.Lee and S.Rhee (2020). Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena. J Biol Chem, 295, 5751-5760. PubMed id: 32198136 DOI: 10.1074/jbc.RA120.012768

Date:

16-Jan-20 Release date: 01-Apr-20

Protein chains

Q8YMD9  (Q8YMD9_NOSS1) -  Bifunctional arginine dihydrolase/ornithine cyclodeaminase AgrE from Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)

Seq: 703 a.a.

Struc: 675 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.3.5.3.27 - arginine dihydrolase.
• Reaction: L-arginine + 2 H2O + 2 H⁺ = L-ornithine + 2 NH4⁺ + CO2
• Enzyme class 3: E.C.4.3.1.12 - ornithine cyclodeaminase.

Pathway:

• Reaction: L-ornithine = L-proline + NH4⁺
• Cofactor: NAD(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.RA120.012768

J Biol Chem 295:5751-5760 (2020)

PubMed id: 32198136

Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena.

H.Lee, S.Rhee.

ABSTRACT

In cyanobacteria, metabolic pathways that use the nitrogen-rich amino acid arginine play a pivotal role in nitrogen storage and mobilization. The N-terminal domains of two recently identified bacterial enzymes: ArgZ from Synechocystis and AgrE from Anabaena, have been found to contain an arginine dihydrolase. This enzyme provides catabolic activity that converts arginine to ornithine, resulting in concomitant release of CO₂ and ammonia. In Synechocystis, the ArgZ-mediated ornithine-ammonia cycle plays a central role in nitrogen storage and remobilization. The C-terminal domain of AgrE contains an ornithine cyclodeaminase responsible for the formation of proline from ornithine and ammonia production, indicating that AgrE is a bifunctional enzyme catalyzing two sequential reactions in arginine catabolism. Here, the crystal structures of AgrE in three different ligation states revealed that it has a tetrameric conformation, possesses a binding site for the arginine dihydrolase substrate l-arginine and product l-ornithine, and contains a binding site for the coenzyme NAD(H) required for ornithine cyclodeaminase activity. Structure-function analyses indicated that the structure and catalytic mechanism of arginine dihydrolase in AgrE are highly homologous with those of a known bacterial arginine hydrolase. We found that in addition to other active-site residues, Asn-71 is essential for AgrE's dihydrolase activity. Further analysis suggested the presence of a passage for substrate channeling between the two distinct AgrE active sites, which are situated ∼45 Å apart. These results provide structural and functional insights into the bifunctional arginine dihydrolase-ornithine cyclodeaminase enzyme AgrE required for arginine catabolism in Anabaena.