DB code: M00170

CATH domain 3.40.50.980 : Rossmann fold
3.40.50.980 : Rossmann fold Catalytic domain
2.30.38.10 : Luciferase; domain 3
3.30.300.30 : GMP Synthetase; Chain A, domain 3 Catalytic domain
-.-.-.- : Catalytic domain
-.-.-.- : Catalytic domain
E.C. 5.1.1.11
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes Pfam
P0C061 Gramicidin S synthetase 1
Gramicidin S synthetase I
ATP-dependent D-phenylalanine adenylase
(D-PheA)
D-phenylalanine activase
Phenylalanine racemase {ATP-hydrolyzing}
EC 5.1.1.11
PF00501 (AMP-binding)
PF00668 (Condensation)
PF00550 (PP-binding)
[Graphical View]
P0C062 Gramicidin S synthetase 1
Gramicidin S synthetase I
ATP-dependent D-phenylalanine adenylase
(D-PheA)
D-phenylalanine activase
Phenylalanine racemase {ATP-hydrolyzing}
EC 5.1.1.11
PF00501 (AMP-binding)
PF00668 (Condensation)
PF00550 (PP-binding)
[Graphical View]

KEGG enzyme name
phenylalanine racemase (ATP-hydrolysing)
phenylalanine racemase
phenylalanine racemase (adenosine triphosphate-hydrolysing)
gramicidin S synthetase I

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0C061 GRSA_ANEMI ATP + L-phenylalanine + H(2)O = AMP + diphosphate + D-phenylalanine. Large multienzyme complex of grsA and grsB. Binds 1 phosphopantetheine covalently.
P0C062 GRSA_BREBE ATP + L-phenylalanine + H(2)O = AMP + diphosphate + D-phenylalanine. Large multienzyme complex of grsA and grsB (By similarity). Binds 1 phosphopantetheine covalently (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00360 Phenylalanine metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C01134 C00305 C00002 C00079 C00001 C00020 C00013 C02265
E.C.
Compound Phosphopantetheine Magnesium ATP L-Phenylalanine H2O AMP Pyrophosphate D-Phenylalanine
Type carbohydrate,peptide/protein,phosphate group/phosphate ion,sulfhydryl group divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids,aromatic ring (only carbon atom) H2O amine group,nucleotide phosphate group/phosphate ion amino acids,aromatic ring (only carbon atom)
ChEBI 4222
18420
15422
17295
58095
15377
16027
29888
16998
57981
PubChem 115254
888
5957
6140
6925665
22247451
962
6083
1023
21961011
6919011
71567
1amuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1amuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1amuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_MG Unbound Bound:PHE Bound:AMP Unbound Unbound
1amuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:_MG Unbound Bound:PHE Bound:AMP Unbound Unbound
1amuA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1amuB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1amuA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1amuB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [3]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1amuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1amuB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1amuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 327(Magnesium binding) THR 326
1amuB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 327(Magnesium binding) THR 326
1amuA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1amuB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1amuA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 517
1amuB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 517

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
Fig.1, Fig.3
[7]
Fig.1
[8]
Fig.1

References
[1]
Resource
Comments
Medline ID
PubMed ID 7309699
Journal J Biochem (Tokyo)
Year 1981
Volume 90
Pages 765-71
Authors Kanda M, Hori K, Kurotsu T, Miura S, Yamada Y, Saito Y
Title Sulfhydryl groups related to the catalytic activity of gramicidin S synthetase 1 of Bacillus brevis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6188751
Journal J Biochem (Tokyo)
Year 1983
Volume 93
Pages 177-88
Authors Hori K, Kanda M, Miura S, Yamada Y, Saito Y
Title Transfer of D-phenylalanine from gramicidin S synthetase 1 to gramicidin S synthetase 2 in gramicidin S synthesis.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 17-530, AND REVISION TO 335.
Medline ID 97392447
PubMed ID 9250661
Journal EMBO J
Year 1997
Volume 16
Pages 4174-83
Authors Conti E, Stachelhaus T, Marahiel MA, Brick P
Title Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S.
Related PDB 1amu
Related UniProtKB P0C061
[4]
Resource
Comments
Medline ID
PubMed ID 9246644
Journal J Protein Chem
Year 1997
Volume 16
Pages 557-64
Authors Vater J, Stein T, Vollenbroich D, Kruft V, Wittmann-Liebold B, Franke P, Liu L, Zuber P
Title The modular organization of multifunctional peptide synthetases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10801328
Journal Biochemistry
Year 2000
Volume 39
Pages 5775-87
Authors Stachelhaus T, Walsh CT
Title Mutational analysis of the epimerization domain in the initiation module PheATE of gramicidin S synthetase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 10712928
Journal Chem Biol
Year 2000
Volume 7
Pages 211-24
Authors Challis GL, Ravel J, Townsend CA
Title Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11330995
Journal Biochemistry
Year 2001
Volume 40
Pages 5329-37
Authors Luo L, Walsh CT
Title Kinetic analysis of three activated phenylalanyl intermediates generated by the initiation module PheATE of gramicidin S synthetase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11697963
Journal J Am Chem Soc
Year 2001
Volume 123
Pages 11208-18
Authors Luo L, Burkart MD, Stachelhaus T, Walsh CT
Title Substrate recognition and selection by the initiation module PheATE of gramicidin S synthetase.
Related PDB
Related UniProtKB

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.

Created Updated
2005-06-15 2009-02-26