DB code: S00440

RLCP classification 3.1244.220200.43 : Transfer
CATH domain 3.75.10.10 : L-arginine/glycine Amidinotransferase; Chain A Catalytic domain
E.C. 2.1.4.1
CSA 1jdw
M-CSA 1jdw
MACiE M0018

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P50440 Glycine amidinotransferase, mitochondrial
EC 2.1.4.1
L-arginine:glycine amidinotransferase
Transamidinase
AT
NP_001473.1 (Protein)
NM_001482.2 (DNA/RNA sequence)
PF02274 (Amidinotransf)
[Graphical View]

KEGG enzyme name
glycine amidinotransferase
arginine-glycine amidinotransferase
arginine-glycine transamidinase
glycine transamidinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P50440 GATM_HUMAN L-arginine + glycine = L-ornithine + guanidinoacetate. Homodimer. There is an equilibrium between the monomeric and dimeric forms, shifted towards the side of the monomer. Mitochondrion 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.

KEGG Pathways
Map code Pathways E.C.
MAP00220 Urea cycle and metabolism of amino groups
MAP00260 Glycine, serine and threonine metabolism
MAP00330 Arginine and proline metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00062 C00037 C00077 C00581
E.C.
Compound L-Arginine Glycine L-Ornithine Guanidinoacetate
Type amino acids,amine group,imine group,lipid amino acids amino acids,amine group,lipid amino acids,amine group,imine group
ChEBI 16467
15428
57305
15729
16344
57742
PubChem 28782
6322
5257127
750
6262
88747248
3946848
4546993
763
1jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1jdxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2jdxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ORN Unbound
4jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:ARG Unbound Unbound Unbound
5jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GLY Unbound Unbound
6jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:ABU Unbound Unbound
7jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:DAV Unbound Unbound
8jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
9jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P50440 & literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
1jdxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
2jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
2jdxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407 deletion M302
3jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
4jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305; mutant C407A
5jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
6jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
7jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
8jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407
9jdwA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 170;ASP 254;HIS 303;ASP 305;CYS 407

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.9 p.3380
[3]
p.196
[4]
p.488-489
[5]
Fig.8 p.17670-17671

References
[1]
Resource
Comments ACTIVE SITE CYS-407
Medline ID 97220385
PubMed ID 9148748
Journal Biochem J
Year 1997
Volume 322
Pages 771-6
Authors Humm A, Fritsche E, Mann K, Gohl M, Huber R
Title Recombinant expression and isolation of human L-arginine:glycine amidinotransferase and identification of its active-site cysteine residue.
Related PDB
Related UniProtKB P50440
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 64-423
Medline ID 97361819
PubMed ID 9218780
Journal EMBO J
Year 1997
Volume 16
Pages 3373-85
Authors Humm A, Fritsche E, Steinbacher S, Huber R
Title Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
Related PDB 1jdw 2jdw 3jdw 4jdw
Related UniProtKB P50440
[3]
Resource
Comments REVIEW
Medline ID 97307728
PubMed ID 9165070
Journal Biol Chem
Year 1997
Volume 378
Pages 193-7
Authors Humm A, Fritsche E, Steinbacher S
Title Structure and reaction mechanism of L-arginine:glycine amidinotransferase.
Related PDB
Related UniProtKB P50440
[4]
Resource
Comments
Medline ID
PubMed ID 9266688
Journal Eur J Biochem
Year 1997
Volume 247
Pages 483-90
Authors Fritsche E, Humm A, Huber R
Title Substrate binding and catalysis by L-arginine:glycine amidinotransferase--a mutagenesis and crystallographic study.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9922132
Journal Biochemistry
Year 1998
Volume 37
Pages 17664-72
Authors Fritsche E, Bergner A, Humm A, Piepersberg W, Huber R
Title Crystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: an enzyme involved in streptomycin biosynthesis.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 64-423
Medline ID 99115650
PubMed ID 9915841
Journal J Biol Chem
Year 1999
Volume 274
Pages 3026-32
Authors Fritsche E, Humm A, Huber R
Title The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study.
Related PDB 1jdx 2jdx 5jdw 6jdw 7jdw 8jdw 9jdw
Related UniProtKB P50440

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]).

Created Updated
2002-11-22 2009-02-26