EzCatDB: S00440

DB codeS00440
RLCP classification3.1244.220200.43
CATH domainDomain 13.75.10.10Catalytic domain
E.C.2.1.4.1
CSA1jdw
MACiEM0018


Enzyme Name
Swiss-protKEGG

P50440
Protein nameGlycine amidinotransferase, mitochondrialglycine amidinotransferase
arginine-glycine amidinotransferase
arginine-glycine transamidinase
glycine transamidinase
SynonymsEC 2.1.4.1
L-arginine:glycine amidinotransferase
Transamidinase
AT

KEGG pathways
MAP codePathways
MAP00220Urea cycle and metabolism of amino groups
MAP00260Glycine, serine and threonine metabolism
MAP00330Arginine and proline metabolism

Swiss-prot:Accession NumberP50440
Entry nameGATM_HUMAN
ActivityL-arginine + glycine = L-ornithine + guanidinoacetate.
SubunitHomodimer. There is an equilibrium between the monomeric and dimeric forms, shifted towards the side of the monomer.
Subcellular locationMitochondrion inner membrane, Peripheral membrane protein, Intermembrane side (Potential). Cytoplasm. Note=The mitochondrial form is found in the intermembrane space probably attached to the outer side of the inner membrane.
Cofactor


SubstratesProducts
KEGG-idC00062C00037C00077C00581
CompoundL-ArginineGlycineL-OrnithineGuanidinoacetate
Typeamino acids,amine group,imine group,lipidamino acidsamino acids,amine group,lipidamino acids,amine group,imine group
1jdwAUnboundUnboundUnboundUnbound
1jdxAUnboundUnboundUnboundUnbound
2jdwAUnboundUnboundUnboundUnbound
2jdxAUnboundUnboundUnboundUnbound
3jdwAUnboundUnboundBound:ORNUnbound
4jdwABound:ARGUnboundUnboundUnbound
5jdwAUnboundBound:GLYUnboundUnbound
6jdwAUnboundAnalogue:ABUUnboundUnbound
7jdwAUnboundAnalogue:DAVUnboundUnbound
8jdwAUnboundUnboundUnboundUnbound
9jdwAUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P50440 & literature [4]
pdbCatalytic residuescomment
1jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

1jdxAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

2jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

2jdxAASP 170;ASP 254;HIS 303;ASP 305;CYS 407
deletion M302
3jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

4jdwAASP 170;ASP 254;HIS 303;ASP 305;       
mutant C407A
5jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

6jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

7jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

8jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407

9jdwAASP 170;ASP 254;HIS 303;ASP 305;CYS 407


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]Fig.9p.3380
[3]p.196
[4]p.488-489
[5]Fig.8p.17670-17671

references
[1]
CommentsACTIVE SITE CYS-407
Medline ID97220385
PubMed ID9148748
JournalBiochem J
Year1997
Volume322
Pages771-6
AuthorsHumm A, Fritsche E, Mann K, Gohl M, Huber R
TitleRecombinant expression and isolation of human L-arginine:glycine amidinotransferase and identification of its active-site cysteine residue.
Related Swiss-protP50440
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 64-423
Medline ID97361819
PubMed ID9218780
JournalEMBO J
Year1997
Volume16
Pages3373-85
AuthorsHumm A, Fritsche E, Steinbacher S, Huber R
TitleCrystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
Related PDB1jdw,2jdw,3jdw,4jdw
Related Swiss-protP50440
[3]
CommentsREVIEW
Medline ID97307728
PubMed ID9165070
JournalBiol Chem
Year1997
Volume378
Pages193-7
AuthorsHumm A, Fritsche E, Steinbacher S
TitleStructure and reaction mechanism of L-arginine:glycine amidinotransferase.
Related Swiss-protP50440
[4]
PubMed ID9266688
JournalEur J Biochem
Year1997
Volume247
Pages483-90
AuthorsFritsche E, Humm A, Huber R
TitleSubstrate binding and catalysis by L-arginine:glycine amidinotransferase--a mutagenesis and crystallographic study.
[5]
PubMed ID9922132
JournalBiochemistry
Year1998
Volume37
Pages17664-72
AuthorsFritsche E, Bergner A, Humm A, Piepersberg W, Huber R
TitleCrystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: an enzyme involved in streptomycin biosynthesis.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 64-423
Medline ID99115650
PubMed ID9915841
JournalJ Biol Chem
Year1999
Volume274
Pages3026-32
AuthorsFritsche E, Humm A, Huber R
TitleThe ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study.
Related PDB1jdx,2jdx,5jdw,6jdw,7jdw,8jdw,9jdw
Related Swiss-protP50440

comments
The early papers, [2] & [3], proposed a catalytic mechanism as follows:
The thiol group of Cys407, which plays a triple role as nucleophile, acid and base, makes a nucleophilic attack on the positively charged carbon atom of amidino group, and simultaneously protonates the leaving group, the epsilon-imino group of the arginine substrate.
A tetrahedral intermediate is formed, which can be stabilized by the interaction between the guanidino nitrogen atoms and acidic residues, Asp170 and Asp305, and between the epsilon-imino nitrogen and His303. The bond between the epsilon-imino group and the amidino-carbon atom is broken.
After the product of ornithine leaves the active site, another substrate, glycin can enter the site and bind to the amidino-carbon atom of the amidino-cysteine. The second half reaction may start with abstarction of proton from the positively charged glycine substrate by His303. The lone electron pair of the glycine nitorogen atom may make a nucleophilic attack at the amidino-carbon atom. In the final steps, formation of a tetrahedral intermediate and its breakdown by cleavage of the carbon-sulfur bond may occur. However, this second half reaction seemed to be speculative, according to the paper [2].
On the other hand, a more recent paper [4] revised this proposed mechanism. In the newly proposed mechanism, the reaction proceeds as follows:
(1) Asp305 was suggested to act as a catalytic acid-base, by abstracting a thiol proton from the nucleophile, Cys407.
(2) Cys407 makes a nucleophilic attack on the positively charged amidino carbon atom, leading to the formation of tetrahedral intermediate.
(3) The tetrahedral intermediate can be stabilized by the interaction with Asp170 and Asp305.
(4) In contrast, the sidechain of His303 seems to be protonated, activating the leaving group, the epsilon-imino group of arginine, as a general acid.
(5) The breakdown of the tetrahedral intermediate generates the product, ornithine, and the amidino-Cys407.
(6) A second substrate, glycine, binds to the active site as an acceptor group.
(7) Probably, His303 acts as a general base, to activate the acceptor amine group of glycine.
(8) The activated amine group makes a nucleophilic attack on the carbon atom of the planar amidino-Cys407.
(9) Probably, Asp305 acts as a general acid to protonate the leaving Cys407, resulting the formation of the product, guanidino-acetic acid.
(#) During the catalysis, Asp254 may be involved in the stablization and orientation of His303 towards the substrates (see [4]).

createdupdated
2002-11-222009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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