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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Clavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1) (Corynebacterium sepedonicum)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotationSAAS annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotationSAAS annotation

Cofactori

Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathway:ipeptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotationSAAS annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Pathway:ipeptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi281 – 2811Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 1UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 2UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi161 – 21252ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciCMIC31964:GJBN-843-MONOMER.
UniPathwayiUPA00219.
UPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:CMS0834Imported
OrganismiClavibacter michiganensis subsp. sepedonicus (strain ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1) (Corynebacterium sepedonicum)Imported
Taxonomic identifieri31964 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaMicrococcalesMicrobacteriaceaeClavibacter
ProteomesiUP000001318 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi31964.CMS_0834.

Structurei

3D structure databases

ProteinModelPortaliB0RF18.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini135 – 327193ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG1181.
KOiK01921.
OMAiDEITCPI.
OrthoDBiEOG6ND0KB.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR000291. D-Ala_lig_Van_CS.
IPR005905. D_ala_D_ala.
IPR011095. Dala_Dala_lig_C.
IPR011127. Dala_Dala_lig_N.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B0RF18-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRISVLFGGE SEERDVSIAS AAQVVPALRQ LGHEVVAVDT AHGALDAAAE
60 70 80 90 100
ARILTPDVGL HPPTSAELAT ASAGGSGAVL RLPADLRDSD LVFLALHGGS
110 120 130 140 150
GEDGRLQALL ELAGIPFTGS GSLGSALAMD KDVAKTLLRA GGVRTPDWLI
160 170 180 190 200
DPEPGAVEAA LGFPVVVKPT GQGSTVGLSV VRAAADLPAA LELAARHGTV
210 220 230 240 250
MVERFVRGRE LTVGVLDGEA LAVGEIGVPV DEAFTYAAKY QAGAIAETFP
260 270 280 290 300
ADLPSEVAEE ARAAALAAHR ILRLDGYSRS DFRLDDAGIL WIIEANSLPG
310 320 330
LTATSLLPQS AAAVGIGYAE LCERIARVVL RGRAG
Length:335
Mass (Da):34,310
Last modified:April 8, 2008 - v1
Checksum:i15182CD4087C75FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM849034 Genomic DNA. Translation: CAQ00951.1.
RefSeqiWP_012298255.1. NC_010407.1.

Genome annotation databases

EnsemblBacteriaiCAQ00951; CAQ00951; CMS0834.
KEGGicms:CMS_0834.
PATRICi21458662. VBIClaMic4666_0892.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM849034 Genomic DNA. Translation: CAQ00951.1.
RefSeqiWP_012298255.1. NC_010407.1.

3D structure databases

ProteinModelPortaliB0RF18.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi31964.CMS_0834.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAQ00951; CAQ00951; CMS0834.
KEGGicms:CMS_0834.
PATRICi21458662. VBIClaMic4666_0892.

Phylogenomic databases

eggNOGiCOG1181.
KOiK01921.
OMAiDEITCPI.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciCMIC31964:GJBN-843-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig.
InterProiIPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR000291. D-Ala_lig_Van_CS.
IPR005905. D_ala_D_ala.
IPR011095. Dala_Dala_lig_C.
IPR011127. Dala_Dala_lig_N.
IPR016185. PreATP-grasp_dom.
[Graphical view]
PANTHERiPTHR23132. PTHR23132. 1 hit.
PfamiPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
[Graphical view]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation."
    Bentley S.D., Corton C., Barron A., Clark L., Doggett J., Harris B., Ormond D., Quail M.A., Brown S.E., Knudson D., Francis D., Parkhill P., Ishimaru C.
    J. Bacteriol. 190:2150-2160(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33113 / DSM 20744 / JCM 9667 / LMG 2889 / C-1Imported.

Entry informationi

Entry nameiB0RF18_CLAMS
AccessioniPrimary (citable) accession number: B0RF18
Entry historyi
Integrated into UniProtKB/TrEMBL: April 8, 2008
Last sequence update: April 8, 2008
Last modified: July 22, 2015
This is version 62 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3

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 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.