EzCatDB: D00108
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DB codeD00108
RLCP classification6.30.97700.5320 : Double-bonded atom exchange
8.211.591510.5526 : Isomerization
6.20.85200.5520 : Double-bonded atom exchange
6.10.82600.5900 : Double-bonded atom exchange
8.211.591510.5527 : Isomerization
6.40.521000.5530 : Double-bonded atom exchange
CATH domainDomain 13.90.1150.10 : Aspartate Aminotransferase, domain 1
Domain 23.40.640.10 : Aspartate Aminotransferase; domain 2Catalytic domain
E.C.2.6.1.57
CSA1ay4

CATH domainRelated DB codes (homologues)
3.40.640.10 : Aspartate Aminotransferase; domain 2D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00109,D00255,D00257,D00258,D00265,D00269,D00515,M00031,D00279
3.90.1150.10 : Aspartate Aminotransferase, domain 1D00085,D00092,D00101,D00102,D00103,D00104,D00107,D00109,D00255,D00257,D00258,D00265,D00269,D00515,M00031,D00279

Enzyme Name
UniProtKBKEGG

P95468P04693
Protein nameAromatic-amino-acid aminotransferaseAromatic-amino-acid aminotransferasearomatic-amino-acid transaminase
aromatic amino acid aminotransferase
aromatic aminotransferase
ArAT
SynonymsARAT
AROAT
EC 2.6.1.57
ARAT
AROAT
EC 2.6.1.57
RefSeq
NP_418478.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492197.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00155 (Aminotran_1_2)
[Graphical view]
PF00155 (Aminotran_1_2)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00271Methionine metabolism
MAP00350Tyrosine metabolism
MAP00360Phenylalanine metabolism
MAP00400Phenylalanine, tyrosine and tryptophan biosynthesis
MAP00401Novobiocin biosynthesis
MAP00950Alkaloid biosynthesis I

UniProtKB:Accession NumberP95468P04693
Entry nameTYRB_PARDETYRB_ECOLI
ActivityAn aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate.An aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate.
SubunitHomodimer.Homodimer.
Subcellular locationCytoplasm.Cytoplasm.
CofactorPyridoxal phosphate.Pyridoxal phosphate.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00018C01021C00026C00972C00025I00027I00036I00028
C00647I00006I00033I00007
CompoundPyridoxal phosphateAromatic amino acid2-OxoglutarateAromatic oxo acidL-GlutamateExternal aldimine intermediate (initial stage:PLP-aromatic amino acid)Quinonoid intermediate-1 (PLP-aromatic amino acid)Ketimine intermediate-1 (PLP-aromatic amino acid)Tetrahedral intermediate from ketimine to PMP Pyridoxamine phosphate (PMP)Ketimine intermediate-2 (PLP-Glu)Quinonoid intermediate-2 (PLP-Glu)External aldimine intermediate (final stage:PLP-Glu)
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamino acids,aromatic ring (only carbon atom)carbohydrate,carboxyl grouparomatic ring (only carbon atom),carbohydrate,carboxyl groupamino acids,carboxyl group







ChEBI18405

30915

16015








PubChem1051

51

88747398
44272391
33032








                     
1ay4A01UnboundUnboundUnboundUnboundUnbound        
1ay4B01UnboundUnboundUnboundUnboundUnbound        
1ay5A01UnboundUnboundUnboundUnboundUnbound        
1ay5B01UnboundUnboundUnboundUnboundUnbound        
1ay8A01UnboundUnboundUnboundUnboundUnbound        
1ay8B01UnboundUnboundUnboundUnboundUnbound        
2ay1A01UnboundUnboundUnboundUnboundUnbound        
2ay1B01UnboundUnboundUnboundUnboundUnbound        
2ay2A01UnboundUnboundUnboundUnboundUnbound        
2ay2B01UnboundUnboundUnboundUnboundUnbound        
2ay3A01UnboundUnboundUnboundUnboundUnbound        
2ay3B01UnboundUnboundUnboundUnboundUnbound        
2ay4A01UnboundUnboundUnboundUnboundUnbound        
2ay4B01UnboundUnboundUnboundUnboundUnbound        
2ay5A01UnboundUnboundUnboundUnboundUnbound        
2ay5B01UnboundUnboundUnboundUnboundUnbound        
2ay6A01UnboundUnboundUnboundUnboundUnbound        
2ay6B01UnboundUnboundUnboundUnboundUnbound        
2ay7A01UnboundUnboundUnboundUnboundUnbound        
2ay7B01UnboundUnboundUnboundUnboundUnbound        
2ay8A01UnboundUnboundUnboundUnboundUnbound        
2ay8B01UnboundUnboundUnboundUnboundUnbound        
2ay9A01UnboundUnboundUnboundUnboundUnbound        
2ay9B01UnboundUnboundUnboundUnboundUnbound        
3tatA01UnboundUnboundUnboundUnboundUnbound        
3tatB01UnboundUnboundUnboundUnboundUnbound        
3tatC01UnboundUnboundUnboundUnboundUnbound        
3tatD01UnboundUnboundUnboundUnboundUnbound        
3tatE01UnboundUnboundUnboundUnboundUnbound        
3tatF01UnboundUnboundUnboundUnboundUnbound        
1ay4A02Bound:PLPUnboundUnboundUnboundUnbound        
1ay4B02Bound:PLPUnboundUnboundUnboundUnbound        
1ay5A02Bound:PLPUnboundUnboundUnboundAnalogue:MAE        
1ay5B02Bound:PLPUnboundUnboundUnboundAnalogue:MAE        
1ay8A02Bound:PLPUnboundUnboundUnboundUnbound        
1ay8B02Bound:PLPAnalogue:HCIUnboundUnboundUnbound        
2ay1A02Bound:PLPUnboundUnboundUnboundUnbound        
2ay1B02Bound:PLPAnalogue:AHCUnboundUnboundUnbound        
2ay2A02Bound:PLPUnboundUnboundUnboundUnbound        
2ay2B02Bound:PLPAnalogue:CXPUnboundUnboundUnbound        
2ay3A02Bound:PLPAnalogue:MPPUnboundUnboundUnbound        
2ay3B02Bound:PLPAnalogue:MPPUnboundUnboundUnbound        
2ay4A02Bound:PLPUnboundUnboundUnboundUnbound        
2ay4B02Bound:PLPAnalogue:PPTUnboundUnboundUnbound        
2ay5A02Bound:PLPUnboundUnboundUnboundUnbound        
2ay5B02Bound:PLPAnalogue:IOPUnboundUnboundUnbound        
2ay6A02Bound:PLPUnboundUnboundUnboundUnbound        
2ay6B02Bound:PLPAnalogue:3IBUnboundUnboundUnbound        
2ay7A02Bound:PLPUnboundUnboundUnboundUnbound        
2ay7B02Bound:PLPAnalogue:CLTUnboundUnboundUnbound        
2ay8A02Bound:PLPAnalogue:4TBUnboundUnboundUnbound        
2ay8B02Bound:PLPAnalogue:4TBUnboundUnboundUnbound        
2ay9A02Bound:PLPAnalogue:5PVUnboundUnboundUnbound        
2ay9B02Bound:PLPAnalogue:5PVUnboundUnboundUnbound        
3tatA02Bound:PLPUnboundUnboundUnboundUnbound        
3tatB02Bound:PLPUnboundUnboundUnboundUnbound        
3tatC02Bound:PLPUnboundUnboundUnboundUnbound        
3tatD02Bound:PLPUnboundUnboundUnboundUnbound        
3tatE02Bound:PLPUnboundUnboundUnboundUnbound        
3tatF02Bound:PLPUnboundUnboundUnboundUnbound        

Active-site residues
resource
PDB;1ay4 and literature [2], [5]
pdbCatalytic residuesCofactor-binding residues
          
1ay4A01 
 
1ay4B01 
 
1ay5A01 
 
1ay5B01 
 
1ay8A01 
 
1ay8B01 
 
2ay1A01 
 
2ay1B01 
 
2ay2A01 
 
2ay2B01 
 
2ay3A01 
 
2ay3B01 
 
2ay4A01 
 
2ay4B01 
 
2ay5A01 
 
2ay5B01 
 
2ay6A01 
 
2ay6B01 
 
2ay7A01 
 
2ay7B01 
 
2ay8A01 
 
2ay8B01 
 
2ay9A01 
 
2ay9B01 
 
3tatA01 
 
3tatB01 
 
3tatC01 
 
3tatD01 
 
3tatE01 
 
3tatF01 
 
1ay4A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
1ay4B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
1ay5A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
1ay5B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
1ay8A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
1ay8B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay1A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay1B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay2A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay2B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay3A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay3B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay4A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay4B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay5A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay5B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay6A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay6B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay7A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay7B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay8A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay8B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay9A02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
2ay9B02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
3tatA02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
3tatB02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
3tatC02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
3tatD02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
3tatE02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)
3tatF02TYR 70;ASP 222;TYR 225;LYS 258
LYS 258(PLP binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[10]Scheme 1
[12]Fig. 1, p.376
[12]Fig. 2, p.377
[12]Fig. 3, p.378

references
[1]
PubMed ID8218300
JournalBiochemistry
Year1993
Volume32
Pages12229-39
AuthorsHayashi H, Inoue K, Nagata T, Kuramitsu S, Kagamiyama H
TitleEscherichia coli aromatic amino acid aminotransferase: characterization and comparison with aspartate aminotransferase.
[2]
PubMed ID8188625
JournalJ Biochem (Tokyo)
Year1994
Volume115
Pages156-61
AuthorsIwasaki M, Hayashi H, Kagamiyama H
TitleProtonation state of the active-site Schiff base of aromatic amino acid aminotransferase: modulation by binding of ligands and implications for its role in catalysis.
[3]
PubMed ID8639626
JournalBiochemistry
Year1996
Volume35
Pages6754-61
AuthorsHayashi H, Inoue K, Mizuguchi H, Kagamiyama H
TitleAnalysis of the substrate-recognition mode of aromatic amino acid aminotransferase by combined use of quasisubstrates and site-directed mutagenesis: systematic hydroxy-group addition/deletion studies to probe the enzyme-substrate interactions.
[4]
PubMed ID9058208
JournalJ Biochem (Tokyo)
Year1997
Volume121
Pages161-71
AuthorsOue S, Okamoto A, Nakai Y, Nakahira M, Shibatani T, Hayashi H, Kagamiyama H
TitleParacoccus denitrificans aromatic amino acid aminotransferase: a model enzyme for the study of dual substrate recognition mechanism.
[5]
PubMed ID9660802
JournalJ Biol Chem
Year1998
Volume273
Pages18353-64
AuthorsKawaguchi S, Kuramitsu S
TitleThermodynamics and molecular simulation analysis of hydrophobic substrate recognition by aminotransferases.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS)
Medline ID98332746
PubMed ID9665848
JournalJ Mol Biol
Year1998
Volume280
Pages443-61
AuthorsOkamoto A, Nakai Y, Hayashi H, Hirotsu K, Kagamiyama H
TitleCrystal structures of Paracoccus denitrificans aromatic amino acid aminotransferase: a substrate recognition site constructed by rearrangement of hydrogen bond network.
Related PDB1ay4,1ay5,1ay8
Related UniProtKBP95468
[7]
PubMed ID9846749
JournalMicrobiology
Year1998
Volume144
Pages3127-34
AuthorsGu W, Song J, Bonner CA, Xie G, Jensen RA
TitlePhhC is an essential aminotransferase for aromatic amino acid catabolism in Pseudomonas aeruginosa.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID99130247
PubMed ID9930977
JournalBiochemistry
Year1999
Volume38
Pages1176-84
AuthorsOkamoto A, Ishii S, Hirotsu K, Kagamiyama H
TitleThe active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity.
Related PDB2ay1,2ay2,2ay3,2ay4,2ay5,2ay6,2ay7,2ay8,2ay9
Related UniProtKBP95468
[9]
PubMed ID10417420
JournalActa Crystallogr D Biol Crystallogr
Year1999
Volume55
Pages1474-7
AuthorsKo TP, Wu SP, Yang WZ, Tsai H, Yuan HS
TitleCrystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase.
Related PDB3tat
[10]
PubMed ID11112527
JournalBiochemistry
Year2000
Volume39
Pages15418-28
AuthorsIslam MM, Hayashi H, Mizuguchi H, Kagamiyama H
TitleThe substrate activation process in the catalytic reaction of Escherichia coli aromatic amino acid aminotransferase.
[11]
PubMed ID10671523
JournalJ Biol Chem
Year2000
Volume275
Pages4871-9
AuthorsMatsui I, Matsui E, Sakai Y, Kikuchi H, Kawarabayasi Y, Ura H, Kawaguchi S, Kuramitsu S, Harata K
TitleThe molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii.
[12]
PubMed ID11933244
JournalChem Rec
Year2001
Volume1
Pages373-84
AuthorsSoda K, Yoshimura T, Esaki N
TitleStereospecificity for the hydrogen transfer of pyridoxal enzyme reactions.

comments
This enzyme belongs to the Aspartate aminotransferase (AAT) subclass of type-I PLP-dependent enzyme superfamily (Aspartate aminotransferase superfamily; AAT). Although the catalytic mechanism of this enzyme has not been elucidated, it must be similar to that of Aspartate aminotransferase (AAT) (D00101 in EzCatDB), as the catalytic site of this enzyme is completely the same as that.
This enzyme catalyzes transamination, which is composed of the following reactions:
(A) Formation of external aldimine (with amine group of aromatic amino acid),
(B) Isomerization (change in the position of double-bond), forming a ketimine intermediate.
(C) Schiff-base deforming by hydration, releasing the first product, aromatic oxo acid, and PMP.
(D) Schiff-base forming by hydration of PMP with carbonyl group of the second substrate, 2-oxoglutarate, forming a ketimine intermediate again.
(E) Isomerization (change in the position of double-bond).
(F) Formation of internal aldimine, leading to the elimination of the product,L-Glu, from PLP.

createdupdated
2004-03-252009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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