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Information on EC 2.3.2.22 - cyclo(L-leucyl-L-leucyl) synthase and Organism(s) Bacillus licheniformis and UniProt Accession Q65EX3

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EC Tree
     2 Transferases
         2.3 Acyltransferases
             2.3.2 Aminoacyltransferases
                2.3.2.22 cyclo(L-leucyl-L-leucyl) synthase
IUBMB Comments
The reaction proceeds following a ping-pong mechanism forming a covalent intermediate between an active site serine and the first L-leucine residue . The proteins from bacteria of the genus Bacillus also form small amounts of cyclo(L-phenylalanyl-L-leucyl) and cyclo(L-leucyl-L-methionyl) .
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Bacillus licheniformis
UNIPROT: Q65EX3
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The taxonomic range for the selected organisms is: Bacillus licheniformis
The enzyme appears in selected viruses and cellular organisms
Synonyms
CDPS, cLL synthase, cyclo(L-leucyl-L-leucyl) synthase, cyclodileucine synthase, cyclodipeptide synthase, pSHaeC06, Shae-CDPS, YvmC, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
cyclo(L-leucyl-L-leucyl) synthase
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cyclodipeptide synthase
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cLL synthase
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cyclodileucine synthase
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YvmC
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2 L-leucyl-tRNALeu = 2 tRNALeu + cyclo(L-leucyl-L-leucyl)
show the reaction diagram
sequential catalytic mechanism, with the successive attachment of two leucine residues on the enzyme via a conserved serine residue
PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
L-leucyl-tRNALeu:L-leucyl-tRNALeu leucyltransferase (cyclizing)
The reaction proceeds following a ping-pong mechanism forming a covalent intermediate between an active site serine and the first L-leucine residue [2]. The proteins from bacteria of the genus Bacillus also form small amounts of cyclo(L-phenylalanyl-L-leucyl) and cyclo(L-leucyl-L-methionyl) [1].
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
additional information
?
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cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides. Catalytic mechanism, overview
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
CDPSs fall into two subfamilies, NYH and XYP, characterized by the presence of specific sequence signatures. Comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold. The XYP and NYH motifs correspond to two structural solutions to facilitate the reactivity of the catalytic serine residue. The CDPS from Bacillus licheniformis belongs to the NYH subfamily
additional information
CDPSs structure comparisons, comparison of the XYP and NYH enzymes shows that the two subfamilies mainly differ in the first half of their Rossmann fold, overview. The CDPS adopts a common architecture with a monomer built around a Rossmann fold domain that displays structural similarity to the catalytic domain of the two class Ic aminoacyl-tRNA synthetases (aaRSs), TyrRS and TrpRS. It contains a deep surface-accessible pocket P1, the location of which corresponds to that of the aminoacyl-binding pocket of the two aaRSs. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. The XYP and the NYH architectures appear as two solutions to stabilize Y202 and facilitate the reactivity of the catalytic S37. Despite these differences, the key catalytic residues (S37, Y202, Y178 and E182, AlbC numbering) are conserved in all CDPSs and have a same location in the catalytic centre of the enzymes. Residues belonging to the signature sequences play parallel roles in the two subfamilies, contributing to the positioning of the catalytic serine and of the crucial Y202 residue. The mode of action of the signature residues however differs, with a more complex network of hydrogen bonds in NYH enzymes. Notably, the signature residues are located in the two catalytic loops at the switch point between the two halves of the Rossmann fold
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in the apo form and complexed with substrate mimics, at 1.7-2.4 A resolutions. Data show the presence of an aminoacyl-enzyme reaction intermediate, but not a dipeptide tRNA intermediate. Reaction follows a sequential catalytic mechanism, with the successive attachment of two leucine residues on the enzyme via a conserved serine residue
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli strain BL21AI
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene yvmC, recombinant expression in Escherichia coli strain BL21AI, subcloning in Escherichia coli strain DH5alpha
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
cyclodipeptide synthases (CDPSs) use two aminoacyl-tRNAs to catalyze the formation of two peptide bonds leading to cyclodipeptides that can be further used for the synthesis of diketopiperazines
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bonnefond, L.; Arai, T.; Sakaguchi, Y.; Suzuki, T.; Ishitani, R.; Nureki, O.
Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog
Proc. Natl. Acad. Sci. USA
108
3912-3917
2011
Bacillus licheniformis (Q65EX3), Bacillus licheniformis ATCC 14580 (Q65EX3)
Manually annotated by BRENDA team
Bourgeois, G.; Seguin, J.; Babin, M.; Belin, P.; Moutiez, M.; Mechulam, Y.; Gondry, M.; Schmitt, E.
Structural basis for partition of the cyclodipeptide synthases into two subfamilies
J. Struct. Biol.
203
17-26
2018
Bacillus licheniformis (Q65EX3), Bacillus licheniformis ATCC 14580 (Q65EX3), Bacillus licheniformis DSM 13 (Q65EX3), Bacillus licheniformis Gibson 46 (Q65EX3), Bacillus licheniformis JCM 2505 (Q65EX3), Bacillus licheniformis NBRC 12200 (Q65EX3), Bacillus licheniformis NCIMB 9375 (Q65EX3), Bacillus licheniformis NRRL NRS-1264 (Q65EX3), Staphylococcus haemolyticus (Q4L2X9), Staphylococcus haemolyticus JCSC1435 (Q4L2X9)
Manually annotated by BRENDA team