PDBsum entry 1n2m

Lyase

PDB id

1n2m

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Contents

			Protein chains

					(+ 0 more) 159 a.a. *

			Ligands

					MRD ×8

			Waters ×498

* Residue conservation analysis

PDB id:

1n2m

Links

Name:

Lyase

Title:

The s53a proenzyme structure of methanococcus jannaschii.

Structure:

Pyruvoyl-dependent arginine decarboxylase. Chain: a, b, c, d, e, f. Synonym: pvlargdc. Engineered: yes. Mutation: yes. Other_details: proenzyme form

Source:

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

Biol. unit:

Trimer (from PQS)

Resolution:

1.90Å

R-factor:

0.186

R-free:

0.221

Authors:

W.D.Tolbert,D.E.Graham,R.H.White,S.E.Ealick

Key ref:

W.D.Tolbert et al. (2003). Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms. Structure, 11, 285-294. PubMed id: 12623016 DOI: 10.1016/S0969-2126(03)00026-1

Date:

23-Oct-02

Release date:

25-Mar-03

PROCHECK

	Headers

	References

Protein chains

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

Seq: Struc:					165 a.a. 159 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class:

E.C.4.1.1.19 - arginine decarboxylase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

L-arginine + H⁺ = agmatine + CO2

L-arginine	+	H(+)	=	agmatine	+	CO2

Cofactor:

Pyridoxal 5'-phosphate

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

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

reference

DOI no: 10.1016/S0969-2126(03)00026-1	Structure 11:285-294 (2003)
PubMed id: 12623016

Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms.
W.D.Tolbert, D.E.Graham, R.H.White, S.E.Ealick.

ABSTRACT

The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of the processed enzyme unexpectedly contained the reaction product agmatine. The crystal structure confirms that arginine decarboxylase is a homotrimer. The protomer fold is a four-layer alphabetabetaalpha sandwich with topology similar to pyruvoyl-dependent histidine decarboxylase. Highly conserved residues Asn47, Ser52, Ser53, Ile54, and Glu109 are proposed to play roles in the self-processing reaction. Agmatine binding residues include the C terminus of the beta chain (Ser52) from one protomer and the Asp35 side chain and the Gly44 and Val46 carbonyl oxygen atoms from an adjacent protomer. Glu109 is proposed to play a catalytic role in the decarboxylation reaction.

Selected figure(s)



	Figure 3. Figure 3. Stereo View of the Active Site of PvlArgDCThe product agamatine and key residues are shown as ball-and-stick models. Electron density is shown for the agmatine molecule and the pyruvoyl group. Key hydrogen bonds between agmatine and the protein are shown as dashed lines and the donor-acceptor distances are labeled. The figure was generated with BOBSCRIPT [44 and 45] and Raster3D [46].

Figure was selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21208300

H.Trip, N.L.Mulder, F.P.Rattray, and J.S.Lolkema (2011).
HdcB, a novel enzyme catalysing maturation of pyruvoyl-dependent histidine decarboxylase.

Mol Microbiol, 79, 861-871.

19997761

S.Bale, and S.E.Ealick (2010).
Structural biology of S-adenosylmethionine decarboxylase.

Amino Acids, 38, 451-460.

19607664

T.N.Giles, D.J.Fisher, and D.E.Graham (2009).
Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains.

BMC Evol Biol, 9, 166.

19255484

X.Y.Liu, J.Lei, X.Liu, X.D.Su, and L.Li (2009).
Preliminary X-ray crystallographic studies of Bacillus subtilis SpeA protein.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 282-284.

18096851

L.L.Grochowski, and R.H.White (2008).
Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea.

Ann N Y Acad Sci, 1125, 190-214.

18650422

T.N.Giles, and D.E.Graham (2008).
Crenarchaeal arginine decarboxylase evolved from an S-adenosylmethionine decarboxylase enzyme.

J Biol Chem, 283, 25829-25838.

15150268

A.V.Toms, C.Kinsland, D.E.McCloskey, A.E.Pegg, and S.E.Ealick (2004).
Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase.

J Biol Chem, 279, 33837-33846.

PDB codes:

1tlu 1tmi

14651609

F.Baunaure, P.Eldin, A.M.Cathiard, and H.Vial (2004).
Characterization of a non-mitochondrial type I phosphatidylserine decarboxylase in Plasmodium falciparum.

Mol Microbiol, 51, 33-46.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.