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Protein

Cyclo(L-leucyl-L-leucyl) synthase

Gene

yvmC

Organism
Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the biosynthesis of pulcherrimin, a red extracellular pigment. It uses activated amino acids in the form of aminoacyl-tRNAs (aa-tRNAs) as substrates to catalyze the ATP-independent formation of cyclodipeptides which are intermediates in diketopiperazine (DKP) biosynthetic pathways. Catalyzes the formation of cyclo(L-Leu-L-Leu) (cLL) from L-leucyl-tRNA(Leu). Can also incorporate various nonpolar residues, such as L-phenylalanine, L-leucine and methionine, into cyclodipeptides.2 Publications

Catalytic activityi

2 L-leucyl-tRNA(Leu) = 2 tRNA(Leu) + cyclo(L-leucyl-L-leucyl).2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei37 – 371Nucleophile1 Publication
Binding sitei40 – 401Substrate
Sitei40 – 401Could have a critical role in the catalytic mechanism
Sitei88 – 881Could be involved in aa-tRNA binding
Sitei98 – 981Could be involved in aa-tRNA binding
Sitei180 – 1801Could be involved in aa-tRNA binding
Sitei184 – 1841Could have a critical role in the catalytic mechanism
Binding sitei204 – 2041Substrate

GO - Molecular functioni

  • transferase activity, transferring amino-acyl groups Source: UniProtKB

GO - Biological processi

  • pigment biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Enzyme and pathway databases

BioCyciBLIC279010:GJ2P-3526-MONOMER.
BRENDAi2.3.2.22. 669.

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclo(L-leucyl-L-leucyl) synthase (EC:2.3.2.22)
Alternative name(s):
Cyclodileucine synthase
Cyclodipeptide synthase
Short name:
CDPS
Gene namesi
Name:yvmC
Ordered Locus Names:BL00817, BLi03566
OrganismiBacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)
Taxonomic identifieri279010 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000000606 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi37 – 371S → A: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication
Mutagenesisi37 – 371S → C: Lack of intermediate formation. 1 Publication
Mutagenesisi40 – 401N → D: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication
Mutagenesisi88 – 881K → A: Strong decrease of L-leucyl-tRNA(Leu) binding, but moderate decrease in the cyclodileucine synthase activity; when associated with A-98. 1 Publication
Mutagenesisi98 – 981R → A: Strong decrease of L-leucyl-tRNA(Leu) binding, but moderate decrease in the cyclodileucine synthase activity; when associated with A-88. 1 Publication
Mutagenesisi158 – 1581R → A: Moderate decrease in the cyclodileucine synthase activity. 1 Publication
Mutagenesisi180 – 1801Y → A: Moderate decrease in the cyclodileucine synthase activity. 1 Publication
Mutagenesisi180 – 1801Y → F: Strong decrease of L-leucyl-tRNA(Leu) binding. 1 Publication
Mutagenesisi184 – 1841E → A: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication
Mutagenesisi184 – 1841E → Q: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication
Mutagenesisi204 – 2041Y → A: Strong decrease in the cyclodileucine synthase activity. 1 Publication
Mutagenesisi204 – 2041Y → F: Strong decrease in the cyclodileucine synthase activity. 1 Publication
Mutagenesisi205 – 2051H → E: Strong decrease of L-leucyl-tRNA(Leu) binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 249249Cyclo(L-leucyl-L-leucyl) synthasePRO_0000423351Add
BLAST

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi279010.BLi03566.

Structurei

Secondary structure

1
249
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 196Combined sources
Helixi20 – 289Combined sources
Beta strandi31 – 366Combined sources
Helixi45 – 5814Combined sources
Beta strandi60 – 667Combined sources
Helixi71 – 777Combined sources
Helixi82 – 10726Combined sources
Beta strandi114 – 1163Combined sources
Turni117 – 1226Combined sources
Helixi124 – 13916Combined sources
Helixi141 – 16121Combined sources
Helixi171 – 19525Combined sources
Beta strandi200 – 2067Combined sources
Helixi209 – 2157Combined sources
Beta strandi227 – 2337Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3OQHX-ray1.90A/B1-249[»]
3OQIX-ray1.70A/B1-249[»]
3OQJX-ray2.40A/B1-249[»]
3S7TX-ray2.81A/B1-249[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ65EX3.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni180 – 1845Substrate binding
Regioni209 – 2102Substrate binding

Sequence similaritiesi

Belongs to the CDPS family.Curated

Phylogenomic databases

eggNOGiENOG410625E. Bacteria.
ENOG41129XG. LUCA.
HOGENOMiHOG000134701.
KOiK17485.
OMAiLAVEYVI.
OrthoDBiEOG6H7FDD.

Family and domain databases

InterProiIPR030903. CDPS.
[Graphical view]
PfamiPF16715. CDPS. 1 hit.
[Graphical view]
TIGRFAMsiTIGR04539. tRNA_cyclodipep. 1 hit.

Sequencei

Sequence statusi: Complete.

Q65EX3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTELIMESKH QLFKTETLTQ NCNEILKRRR HVLVGISPFN SRFSEDYIHR
60 70 80 90 100
LIAWAVREFQ SVSVLLAGKE AANLLEALGT PHGKAERKVR KEVSRNRRFA
110 120 130 140 150
EKALEAHGGN PEDIHTFSDF ANQTAYRNLR MEVEAAFFDQ THFRNACLEM
160 170 180 190 200
SHAAILGRAR GTRMDVVEVS ADMLELAVEY VIAELPFFIA APDILGVEET
210 220 230 240
LLAYHRPWKL GEQISRNEFA VKMRPNQGYL MVSEADERVE SKSMQEERV
Length:249
Mass (Da):28,550
Last modified:October 25, 2004 - v1
Checksum:i9E66BB41B7DFB2BF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000002 Genomic DNA. Translation: AAU25020.1.
AE017333 Genomic DNA. Translation: AAU42391.1.
RefSeqiWP_009329597.1. NC_006322.1.

Genome annotation databases

EnsemblBacteriaiAAU25020; AAU25020; BL00817.
AAU42391; AAU42391; BLi03566.
GeneIDi3028664.
KEGGibld:BLi03566.
bli:BL00817.
PATRICi18952904. VBIBacLic203714_3628.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000002 Genomic DNA. Translation: AAU25020.1.
AE017333 Genomic DNA. Translation: AAU42391.1.
RefSeqiWP_009329597.1. NC_006322.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3OQHX-ray1.90A/B1-249[»]
3OQIX-ray1.70A/B1-249[»]
3OQJX-ray2.40A/B1-249[»]
3S7TX-ray2.81A/B1-249[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi279010.BLi03566.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAU25020; AAU25020; BL00817.
AAU42391; AAU42391; BLi03566.
GeneIDi3028664.
KEGGibld:BLi03566.
bli:BL00817.
PATRICi18952904. VBIBacLic203714_3628.

Phylogenomic databases

eggNOGiENOG410625E. Bacteria.
ENOG41129XG. LUCA.
HOGENOMiHOG000134701.
KOiK17485.
OMAiLAVEYVI.
OrthoDBiEOG6H7FDD.

Enzyme and pathway databases

BioCyciBLIC279010:GJ2P-3526-MONOMER.
BRENDAi2.3.2.22. 669.

Miscellaneous databases

EvolutionaryTraceiQ65EX3.

Family and domain databases

InterProiIPR030903. CDPS.
[Graphical view]
PfamiPF16715. CDPS. 1 hit.
[Graphical view]
TIGRFAMsiTIGR04539. tRNA_cyclodipep. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46.
  2. "The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential."
    Veith B., Herzberg C., Steckel S., Feesche J., Maurer K.H., Ehrenreich P., Baeumer S., Henne A., Liesegang H., Merkl R., Ehrenreich A., Gottschalk G.
    J. Mol. Microbiol. Biotechnol. 7:204-211(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46.
  3. Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY.
  4. "Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog."
    Bonnefond L., Arai T., Sakaguchi Y., Suzuki T., Ishitani R., Nureki O.
    Proc. Natl. Acad. Sci. U.S.A. 108:3912-3917(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, MUTAGENESIS OF SER-37; ASN-40; LYS-88; ARG-98; ARG-158; TYR-180; GLU-184; TYR-204 AND HIS-205, ACTIVE SITE, REACTION MECHANISM, SUBUNIT.

Entry informationi

Entry nameiCDLS_BACLD
AccessioniPrimary (citable) accession number: Q65EX3
Secondary accession number(s): Q62QE0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 18, 2013
Last sequence update: October 25, 2004
Last modified: January 20, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.