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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Caulobacter segnis (strain ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059) (Mycoplana segnis)
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 bindingi260 – 2601Magnesium or manganese 1UniRule annotation
Metal bindingi274 – 2741Magnesium or manganese 1UniRule annotation
Metal bindingi274 – 2741Magnesium or manganese 2UniRule annotation
Metal bindingi276 – 2761Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18855ATPUniRule 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

BioCyciCSEG509190:GHVG-1167-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:Cseg_1146Imported
OrganismiCaulobacter segnis (strain ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059) (Mycoplana segnis)Imported
Taxonomic identifieri509190 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
ProteomesiUP000002629: 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

ProteinModelPortaliD5VFB6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini107 – 307201ATP-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

HOGENOMiHOG000011592.
KOiK01921.
OMAiARYNPGR.

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. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 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.

D5VFB6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQQPLSGRH IAVLLGGPSS ERKVSLVSGA ECADALERLG AKVTRIDAGP
60 70 80 90 100
DIAQVLTAAK PDLVFNALHG EWGEDGCVQG VLETLKLPYT HSGVLASALA
110 120 130 140 150
MDKAKAKAVL AAAGVVVPGG GLFNRHDVAR DHVLPPPYVV KPNAEGSSVG
160 170 180 190 200
VFIVKEGANR PPEEVGAPSW TFGEEVMVEP YIRGLELAVA VMGEANGPRA
210 220 230 240 250
LAVTDIRAST GFYDYEAKYS EGGSIHVLPA PIPDGVRDRA MRMAELAHTA
260 270 280 290 300
LGCRSVTRSD LRYDDINDIL VLLEVNTQPG MTPTSLAPEQ AAHVGIPFDQ
310
LVLWIVEDAY ARRNAGGTA
Length:319
Mass (Da):33,655
Last modified:July 13, 2010 - v1
Checksum:i8FE06A3AD4A3C0FC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002008 Genomic DNA. Translation: ADG09648.1.
RefSeqiWP_013078315.1. NC_014100.1.
YP_003592266.1. NC_014100.1.

Genome annotation databases

EnsemblBacteriaiADG09648; ADG09648; Cseg_1146.
GeneIDi9102640.
KEGGicse:Cseg_1146.
PATRICi37202315. VBICauSeg118057_1174.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002008 Genomic DNA. Translation: ADG09648.1.
RefSeqiWP_013078315.1. NC_014100.1.
YP_003592266.1. NC_014100.1.

3D structure databases

ProteinModelPortaliD5VFB6.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADG09648; ADG09648; Cseg_1146.
GeneIDi9102640.
KEGGicse:Cseg_1146.
PATRICi37202315. VBICauSeg118057_1174.

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiARYNPGR.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciCSEG509190:GHVG-1167-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. 2 hits.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 21756 / DSM 7131 / JCM 7823 / NBRC 15250 / LMG 17158 / TK0059Imported.

Entry informationi

Entry nameiD5VFB6_CAUST
AccessioniPrimary (citable) accession number: D5VFB6
Entry historyi
Integrated into UniProtKB/TrEMBL: July 13, 2010
Last sequence update: July 13, 2010
Last modified: March 4, 2015
This is version 35 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.