PDBsum entry 1gc2

Lyase

PDB id

1gc2

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Contents

			Protein chains

					373 a.a. *

			Waters ×1189

* Residue conservation analysis

PDB id:

1gc2

Links
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Name:

Lyase

Title:

Crystal structure of the pyridoxal-5'-phosphate dependent l-methionine gamma-lyase from pseudomonas putida

Structure:

Methionine gamma-lyase. Chain: a, b, c, d. Ec: 4.4.1.11

Source:

Pseudomonas putida. Organism_taxid: 303

Biol. unit:

Tetramer (from PQS)

Resolution:

2.00Å

R-factor:

0.211

R-free:

0.243

Authors:

H.Motoshima,K.Inagaki,T.Kumasaka,M.Furuichi,H.Inoue,T.Tamura,N.Esaki, K.Soda,N.Tanaka,M.Yamamoto,H.Tanaka

Key ref:

H.Motoshima et al. (2000). Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida. J Biochem (tokyo), 128, 349-354. PubMed id: 10965031

Date:

06-Jul-00

Release date:

08-May-02

PROCHECK

	Headers

	References

Protein chains

P13254 (MEGL_PSEPU) - L-methionine gamma-lyase from Pseudomonas putida

Seq: Struc:					398 a.a. 373 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class 1:

E.C.4.4.1.11 - methionine gamma-lyase.

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

Reaction:

L-methionine + H2O = methanethiol + 2-oxobutanoate + NH4⁺

L-methionine	+	H2O	=	methanethiol	+	2-oxobutanoate	+	NH4(+)

Cofactor:

Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate

Enzyme class 2:

E.C.4.4.1.2 - homocysteine desulfhydrase.

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

Reaction:

L-homocysteine + H2O = 2-oxobutanoate + hydrogen sulfide + NH4⁺ + H⁺

L-homocysteine	+	H2O	=	2-oxobutanoate	+	hydrogen sulfide	+	NH4(+)	+	H(+)

Cofactor:

Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate

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

	J Biochem (tokyo) 128:349-354 (2000)
PubMed id: 10965031

Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida.
H.Motoshima, K.Inagaki, T.Kumasaka, M.Furuichi, H.Inoue, T.Tamura, N.Esaki, K.Soda, N.Tanaka, M.Yamamoto, H.Tanaka.

ABSTRACT

L-Methionine gamma-lyase (MGL) catalyzes the pyridoxal 5'-phosphate (PLP) dependent alpha,gamma-elimination of L-methionine. We have determined two crystal structures of MGL from Pseudomonas putida using MAD (multiwavelength anomalous diffraction) and molecular replacement methods. The structures have been refined to an R-factor of 21.1% at 2.0 and 1.7 A resolution using synchrotron radiation diffraction data. A homotetramer with 222 symmetry is built up by non-crystallographic symmetry. Two monomers associate to build the active dimer. The spatial fold of subunits, with three functionally distinct domains and their quarternary arrangement, is similar to those of L-cystathionine beta-lyase and L-cystathionine gamma-synthase from Escherichia coli.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20146062

A.S.El-Sayed (2010).
Microbial L-methioninase: production, molecular characterization, and therapeutic applications.

Appl Microbiol Biotechnol, 86, 445-467.

18219122

A.Nikulin, S.Revtovich, E.Morozova, N.Nevskaya, S.Nikonov, M.Garber, and T.Demidkina (2008).
High-resolution structure of methionine gamma-lyase from Citrobacter freundii.

Acta Crystallogr D Biol Crystallogr, 64, 211-218.

PDB code:

2rfv

18678935

D.Sato, T.Karaki, A.Shimizu, K.Kamei, S.Harada, and T.Nozaki (2008).
Crystallization and preliminary X-ray analysis of L-methionine gamma-lyase 1 from Entamoeba histolytica.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 697-699.

17169919

A.Goyer, E.Collakova, Y.Shachar-Hill, and A.D.Hanson (2007).
Functional characterization of a methionine gamma-lyase in Arabidopsis and its implication in an alternative to the reverse trans-sulfuration pathway.

Plant Cell Physiol, 48, 232-242.

17223627

V.Ali, and T.Nozaki (2007).
Current therapeutics, their problems, and sulfur-containing-amino-acid metabolism as a novel target against infections by "amitochondriate" protozoan parasites.

Clin Microbiol Rev, 20, 164-187.

17012806

D.Sato, W.Yamagata, K.Kamei, T.Nozaki, and S.Harada (2006).
Expression, purification and crystallization of L-methionine gamma-lyase 2 from Entamoeba histolytica.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1034-1036.

16615855

I.V.Manukhov, D.V.Mamaeva, E.A.Morozova, S.M.Rastorguev, N.G.Faleev, T.V.Demidkina, and G.B.Zavilgelsky (2006).
L-methionine gamma-lyase from Citrobacter freundii: cloning of the gene and kinetic parameters of the enzyme.

Biochemistry (Mosc), 71, 361-369.

16012835

T.Takakura, T.Ito, S.Yagi, Y.Notsu, T.Itakura, T.Nakamura, K.Inagaki, N.Esaki, R.M.Hoffman, and A.Takimoto (2006).
High-level expression and bulk crystallization of recombinant L-methionine gamma-lyase, an anticancer agent.

Appl Microbiol Biotechnol, 70, 183-192.

16511092

D.V.Mamaeva, E.A.Morozova, A.D.Nikulin, S.V.Revtovich, S.V.Nikonov, M.B.Garber, and T.V.Demidkina (2005).
Structure of Citrobacter freundii L-methionine gamma-lyase.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 546-549.

PDB code:

1y4i

15574935

F.Amarita, M.Yvon, M.Nardi, E.Chambellon, J.Delettre, and P.Bonnarme (2004).
Identification and functional analysis of the gene encoding methionine-gamma-lyase in Brevibacterium linens.

Appl Environ Microbiol, 70, 7348-7354.

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 code is shown on the right.