EzCatDB: M00170
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DB codeM00170
CATH domainDomain 13.40.50.980 : Rossmann fold
Domain 23.40.50.980 : Rossmann foldCatalytic domain
Domain 32.30.38.10 : Luciferase; domain 3
Domain 43.30.300.30 : GMP Synthetase; Chain A, domain 3Catalytic domain
Domain 5-.-.-.-Catalytic domain
Domain 6-.-.-.-Catalytic domain
E.C.5.1.1.11

CATH domainRelated DB codes (homologues)
2.30.38.10 : Luciferase; domain 3M00009,M00347
3.30.300.30 : GMP Synthetase; Chain A, domain 3M00009,M00347
3.40.50.980 : Rossmann foldM00009,M00347

Enzyme Name
UniProtKBKEGG

P0C061P0C062
Protein nameGramicidin S synthetase 1Gramicidin S synthetase 1phenylalanine racemase (ATP-hydrolysing)
phenylalanine racemase
phenylalanine racemase (adenosine triphosphate-hydrolysing)
gramicidin S synthetase I
SynonymsGramicidin S synthetase I
Gramicidin S synthetase I
IncludesATP-dependent D-phenylalanine adenylase
(D-PheA)
D-phenylalanine activase
Phenylalanine racemase {ATP-hydrolyzing}
   EC 5.1.1.11
ATP-dependent D-phenylalanine adenylase
(D-PheA)
D-phenylalanine activase
Phenylalanine racemase {ATP-hydrolyzing}
   EC 5.1.1.11
PfamPF00501 (AMP-binding)
PF00668 (Condensation)
PF00550 (PP-binding)
[Graphical view]
PF00501 (AMP-binding)
PF00668 (Condensation)
PF00550 (PP-binding)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00360Phenylalanine metabolism

UniProtKB:Accession NumberP0C061P0C062
Entry nameGRSA_ANEMIGRSA_BREBE
ActivityATP + L-phenylalanine + H(2)O = AMP + diphosphate + D-phenylalanine.ATP + L-phenylalanine + H(2)O = AMP + diphosphate + D-phenylalanine.
SubunitLarge multienzyme complex of grsA and grsB.Large multienzyme complex of grsA and grsB (By similarity).
Subcellular location

CofactorBinds 1 phosphopantetheine covalently.Binds 1 phosphopantetheine covalently (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC01134C00305C00002C00079C00001C00020C00013C02265
CompoundPhosphopantetheineMagnesiumATPL-PhenylalanineH2OAMPPyrophosphateD-Phenylalanine
Typecarbohydrate,peptide/protein,phosphate group/phosphate ion,sulfhydryl groupdivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,aromatic ring (only carbon atom)H2Oamine group,nucleotidephosphate group/phosphate ionamino acids,aromatic ring (only carbon atom)
ChEBI4222
18420
15422
17295
58095
15377
16027
29888
16998
57981
PubChem115254
888
5957
6925665
6140
962
22247451
6083
21961011
1023
71567
6919011
                
1amuA01UnboundUnboundUnboundUnbound UnboundUnboundUnbound
1amuB01UnboundUnboundUnboundUnbound UnboundUnboundUnbound
1amuA02UnboundBound:_MGUnboundBound:PHE Bound:AMPUnboundUnbound
1amuB02UnboundBound:_MGUnboundBound:PHE Bound:AMPUnboundUnbound
1amuA03UnboundUnboundUnboundUnbound UnboundUnboundUnbound
1amuB03UnboundUnboundUnboundUnbound UnboundUnboundUnbound
1amuA04UnboundUnboundUnboundUnbound UnboundUnboundUnbound
1amuB04UnboundUnboundUnboundUnbound UnboundUnboundUnbound

Active-site residues
resource
literature [3]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
1amuA01 
 
 
1amuB01 
 
 
1amuA02 
GLU 327(Magnesium binding)
THR 326
1amuB02 
GLU 327(Magnesium binding)
THR 326
1amuA03 
 
 
1amuB03 
 
 
1amuA04LYS 517
 
 
1amuB04LYS 517
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]Fig.1, Fig.3
[7]Fig.1
[8]Fig.1

references
[1]
PubMed ID7309699
JournalJ Biochem (Tokyo)
Year1981
Volume90
Pages765-71
AuthorsKanda M, Hori K, Kurotsu T, Miura S, Yamada Y, Saito Y
TitleSulfhydryl groups related to the catalytic activity of gramicidin S synthetase 1 of Bacillus brevis.
[2]
PubMed ID6188751
JournalJ Biochem (Tokyo)
Year1983
Volume93
Pages177-88
AuthorsHori K, Kanda M, Miura S, Yamada Y, Saito Y
TitleTransfer of D-phenylalanine from gramicidin S synthetase 1 to gramicidin S synthetase 2 in gramicidin S synthesis.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 17-530, AND REVISION TO 335.
Medline ID97392447
PubMed ID9250661
JournalEMBO J
Year1997
Volume16
Pages4174-83
AuthorsConti E, Stachelhaus T, Marahiel MA, Brick P
TitleStructural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S.
Related PDB1amu
Related UniProtKBP0C061
[4]
PubMed ID9246644
JournalJ Protein Chem
Year1997
Volume16
Pages557-64
AuthorsVater J, Stein T, Vollenbroich D, Kruft V, Wittmann-Liebold B, Franke P, Liu L, Zuber P
TitleThe modular organization of multifunctional peptide synthetases.
[5]
PubMed ID10801328
JournalBiochemistry
Year2000
Volume39
Pages5775-87
AuthorsStachelhaus T, Walsh CT
TitleMutational analysis of the epimerization domain in the initiation module PheATE of gramicidin S synthetase.
[6]
PubMed ID10712928
JournalChem Biol
Year2000
Volume7
Pages211-24
AuthorsChallis GL, Ravel J, Townsend CA
TitlePredictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains.
[7]
PubMed ID11330995
JournalBiochemistry
Year2001
Volume40
Pages5329-37
AuthorsLuo L, Walsh CT
TitleKinetic analysis of three activated phenylalanyl intermediates generated by the initiation module PheATE of gramicidin S synthetase.
[8]
PubMed ID11697963
JournalJ Am Chem Soc
Year2001
Volume123
Pages11208-18
AuthorsLuo L, Burkart MD, Stachelhaus T, Walsh CT
TitleSubstrate recognition and selection by the initiation module PheATE of gramicidin S synthetase.

comments
This enzyme is composed of three functional domains, the N-terminal adenylase domain, acyl carrier domain, and the C-terminal epimerase domain (see [5]). The second acyl carrier domain binds phosphopantetheine covalently.
The structure of the N-terminal domain, which itself has four units, has only been determined so far.
According to the literature [5], [7] & [8], this enzyme catalyzes the following reactions successively.
(A) Transfer of adenylate from ATP to the carboxylate oxygen of L-phenylalanine. (This reaction occurs at the N-terminal domain.)
ATP + L-phenylalanine = L-phenylalanyl-adenosine-5'-phsphate diester.
(B) Transfer of acyl group from the adenylated phenylalanine to thiol group of the phosphopantetheine cofactor on the acyl carrier domain, releasing AMP as leaving group. (This reaction occurs at the acyl carrier domain.)
L-Phenylalanyl-adenosine-5'-phsphate diester + phosphopantetheine-acyl enzyme = L-phenylalanyl-S-4'-phosphopantetheine-acyl enzyme + AMP.
(C) Isomerization (shift of double-bond position)
(C') Isomerization (shift of double-bond position) (These reactions occur on the C-terminal epimerase domain.)
L-phenylalanyl-S-4'-phosphopantetheine-acyl enzyme = D-phenylalanyl-S-4'-phosphopantetheine-acyl enzyme.
(D) Removal of D-phenylalanine from the cofactor. This reaction probably carried out by gramicidin S synthetase II (swiss-prot;P14688), which synthesises gramicidin S.

createdupdated
2005-06-152009-02-26


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