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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)DescriptionActionsGraphical viewLength
Active sitei37Nucleophile1 Publication1
Binding sitei40Substrate1
Sitei40Could have a critical role in the catalytic mechanism1
Sitei88Could be involved in aa-tRNA binding1
Sitei98Could be involved in aa-tRNA binding1
Sitei180Could be involved in aa-tRNA binding1
Sitei184Could have a critical role in the catalytic mechanism1
Binding sitei204Substrate1

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

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)DescriptionActionsGraphical viewLength
Mutagenesisi37S → A: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication1
Mutagenesisi37S → C: Lack of intermediate formation. 1 Publication1
Mutagenesisi40N → D: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication1
Mutagenesisi88K → A: Strong decrease of L-leucyl-tRNA(Leu) binding, but moderate decrease in the cyclodileucine synthase activity; when associated with A-98. 1 Publication1
Mutagenesisi98R → A: Strong decrease of L-leucyl-tRNA(Leu) binding, but moderate decrease in the cyclodileucine synthase activity; when associated with A-88. 1 Publication1
Mutagenesisi158R → A: Moderate decrease in the cyclodileucine synthase activity. 1 Publication1
Mutagenesisi180Y → A: Moderate decrease in the cyclodileucine synthase activity. 1 Publication1
Mutagenesisi180Y → F: Strong decrease of L-leucyl-tRNA(Leu) binding. 1 Publication1
Mutagenesisi184E → A: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication1
Mutagenesisi184E → Q: It is able to bind L-leucyl-tRNA(Leu), but has almost no cyclodileucine synthase activity. 1 Publication1
Mutagenesisi204Y → A: Strong decrease in the cyclodileucine synthase activity. 1 Publication1
Mutagenesisi204Y → F: Strong decrease in the cyclodileucine synthase activity. 1 Publication1
Mutagenesisi205H → E: Strong decrease of L-leucyl-tRNA(Leu) binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004233511 – 249Cyclo(L-leucyl-L-leucyl) synthaseAdd BLAST249

Interactioni

Subunit structurei

Monomer.1 Publication

Protein-protein interaction databases

STRINGi279010.BLi03566.

Structurei

Secondary structure

1249
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi14 – 19Combined sources6
Helixi20 – 28Combined sources9
Beta strandi31 – 36Combined sources6
Helixi45 – 58Combined sources14
Beta strandi60 – 66Combined sources7
Helixi71 – 77Combined sources7
Helixi82 – 107Combined sources26
Beta strandi114 – 116Combined sources3
Turni117 – 122Combined sources6
Helixi124 – 139Combined sources16
Helixi141 – 161Combined sources21
Helixi171 – 195Combined sources25
Beta strandi200 – 206Combined sources7
Helixi209 – 215Combined sources7
Beta strandi227 – 233Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OQHX-ray1.90A/B1-249[»]
3OQIX-ray1.70A/B1-249[»]
3OQJX-ray2.40A/B1-249[»]
3S7TX-ray2.81A/B1-249[»]
SMRiQ65EX3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ65EX3.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni180 – 184Substrate binding5
Regioni209 – 210Substrate binding2

Sequence similaritiesi

Belongs to the CDPS family.Curated

Phylogenomic databases

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

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3OQHX-ray1.90A/B1-249[»]
3OQIX-ray1.70A/B1-249[»]
3OQJX-ray2.40A/B1-249[»]
3S7TX-ray2.81A/B1-249[»]
SMRiQ65EX3.
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.

Enzyme and pathway databases

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...

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: November 2, 2016
This is version 70 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.