PDBsum entry 2qqc

Lyase

PDB id: 2qqc

Contents

Protein chains

46 a.a. *

(+ 0 more) 113 a.a. *

47 a.a. *

50 a.a. *

40 a.a. *

Ligands

AG2 ×6

MPD ×4

Waters ×501

* Residue conservation analysis

PDB id:

2qqc

Name:

Lyase

Title:

E109q mutant of pyruvoyl-dependent arginine decarboxylase from methanococcus jannashii

Structure:

Pyruvoyl-dependent arginine decarboxylase subunit beta. Chain: a, c, e, g, i, k. Fragment: beta subunit. Engineered: yes. Pyruvoyl-dependent arginine decarboxylase subunit alpha. Chain: b, d, f, h, j, l. Fragment: alpha subunit. Engineered: yes. Mutation: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: pdad, mj0316. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.194 R-free: 0.237

Authors:

S.E.Ealick,E.S.Soriano

Key ref:

E.V.Soriano et al. (2008). Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii. Acta Crystallogr D Biol Crystallogr, 64, 377-382. PubMed id: 18391404

Date:

26-Jul-07 Release date: 18-Mar-08

Protein chain

Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 165 a.a.

Struc: 46 a.a.

Protein chains

Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 165 a.a.

Struc: 113 a.a.*

Protein chain

Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 165 a.a.

Struc: 47 a.a.

Protein chain

Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 165 a.a.

Struc: 50 a.a.

Protein chains

Q57764  (PDAD_METJA) -  Pyruvoyl-dependent arginine decarboxylase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 165 a.a.

Struc: 40 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L: E.C.4.1.1.19 - arginine decarboxylase.
• Reaction: L-arginine + H⁺ = agmatine + CO2

L-arginine + H(+) = agmatine (Bound ligand (Het Group name = AG2) corresponds exactly) + CO2

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = MPD) matches with 41.18% similarity)

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

reference

Acta Crystallogr D Biol Crystallogr 64:377-382 (2008)

PubMed id: 18391404

Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii.

E.V.Soriano, D.E.McCloskey, C.Kinsland, A.E.Pegg, S.E.Ealick.

ABSTRACT

Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) catalyzes the first step of the polyamine-biosynthetic pathway in plants and some archaebacteria. The pyruvoyl group of PvlArgDC is generated by an internal autoserinolysis reaction at an absolutely conserved serine residue in the proenzyme, resulting in two polypeptide chains. Based on the native structure of PvlArgDC from Methanococcus jannaschii, the conserved residues Asn47 and Glu109 were proposed to be involved in the decarboxylation and autoprocessing reactions. N47A and E109Q mutant proteins were prepared and the three-dimensional structure of each protein was determined at 2.0 A resolution. The N47A and E109Q mutant proteins showed reduced decarboxylation activity compared with the wild-type PvlArgDC. These residues may also be important for the autoprocessing reaction, which utilizes a mechanism similar to that of the decarboxylation reaction.