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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Lactobacillus crispatus (strain ST1)
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

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation
  • Mg2+, Mn2+Note: Binds 2 magnesium or manganese ions per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi297 – 2971Magnesium or manganese 1UniRule annotation
Metal bindingi310 – 3101Magnesium or manganese 1UniRule annotation
Metal bindingi310 – 3101Magnesium or manganese 2UniRule annotation
Metal bindingi312 – 3121Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi169 – 22456ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
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

BioCyciLCRI748671:GIX1-136-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 annotationImported
Ordered Locus Names:LCRIS_00128Imported
OrganismiLactobacillus crispatus (strain ST1)Imported
Taxonomic identifieri748671 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
ProteomesiUP000002371: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Structurei

3D structure databases

ProteinModelPortaliD5H0P0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini134 – 343210ATP-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

HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D5H0P0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKKLQVGLI FGGNSSEYEV SIVSGHNIYK AIDKDKFDVH PIWITNEGYF
60 70 80 90 100
ANEEESFKVL DDPSYQVKNP HKVNNISNLI ELENLPEIDV FFPIVHGNLG
110 120 130 140 150
EDGVLQGLFR LMDKPFVGDD VLGAAVTMDK EFTKILAQRV GVPVADWISI
160 170 180 190 200
KRFEYDDKKN AKLNYEKVAE KLGRDMFVKP SNQGSSVGVS HVTNADEYTA
210 220 230 240 250
ALKEAFKYDD KVLVEKTVPG TEVETAVLGN DKPIVAGVGQ ITNAKGSFYT
260 270 280 290 300
YENKYDDNST SKLQIPADLP QEIIDTVREN ARKVYAATEC SGMARIDSML
310 320 330 340 350
TPGGKVVLTE VNALPGFTNI SMYPKLFEEA GVPYSELITR LIEAGMDRFD
360
HKKTLLHKHD
Length:360
Mass (Da):40,093
Last modified:June 15, 2010 - v1
Checksum:iE092F4890AD3CB51
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN692037 Genomic DNA. Translation: CBL49575.1.
RefSeqiYP_003600600.1. NC_014106.1.

Genome annotation databases

EnsemblBacteriaiCBL49575; CBL49575; LCRIS_00128.
GeneIDi9105891.
KEGGilcr:LCRIS_00128.
PATRICi37238995. VBILacCri149433_0120.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN692037 Genomic DNA. Translation: CBL49575.1.
RefSeqiYP_003600600.1. NC_014106.1.

3D structure databases

ProteinModelPortaliD5H0P0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCBL49575; CBL49575; LCRIS_00128.
GeneIDi9105891.
KEGGilcr:LCRIS_00128.
PATRICi37238995. VBILacCri149433_0120.

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciLCRI748671:GIX1-136-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ST1Imported.
  2. "Genome Sequence of Lactobacillus crispatus ST1."
    Ojala T., Kuparinen V., Koskinen J.P., Alatalo E., Holm L., Auvinen P., Edelman S., Westerlund-Wikstroem B., Korhonen T.K., Paulin L., Kankainen M.
    Submitted (MAR-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: ST1.

Entry informationi

Entry nameiD5H0P0_LACCS
AccessioniPrimary (citable) accession number: D5H0P0
Entry historyi
Integrated into UniProtKB/TrEMBL: June 15, 2010
Last sequence update: June 15, 2010
Last modified: March 4, 2015
This is version 36 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete 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.