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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rickettsia rickettsii (strain Sheila Smith)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi268 – 2681Magnesium or manganese 1UniRule annotation
Metal bindingi282 – 2821Magnesium or manganese 1UniRule annotation
Metal bindingi282 – 2821Magnesium or manganese 2UniRule annotation
Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi147 – 19953ATPUniRule 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

Ligase

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciRRIC392021:GIY1-359-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:A1G_01910
OrganismiRickettsia rickettsii (strain Sheila Smith)
Taxonomic identifieri392021 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiaspotted fever group
ProteomesiUP000006832 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 321321D-alanine--D-alanine ligasePRO_1000030488Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi392021.A1G_01910.

Structurei

3D structure databases

ProteinModelPortaliA8GRC1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini121 – 315195ATP-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.
HOGENOMiHOG000011592.
KOiK01921.
OMAiKYTEGFA.
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. 2 hits.
[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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A8GRC1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHKYQTHWVE HSIVKILSST GKKHIALMAG GMSAEREVSL VSSEGVSKAL
60 70 80 90 100
IELGYRVTFI DMGADIAVRL QEIKPDIVFN CLHGTYGEDG GLPGLLNIMR
110 120 130 140 150
IPYTHSGVLS SALAFDKIHS RIWFLTNNIN MAESIVVNKS DNIKNDPMKR
160 170 180 190 200
PYVIKPLTQG SSIGVEVIFA EDDFNFADYD FPYGDQVIIE QYIKGRELQV
210 220 230 240 250
AVLNGKALGA LEIKLLKNRF YDYETKYTAG FADHLCPAPL PANLYEKLLI
260 270 280 290 300
ESEKIYKTMN CKGPARAEFI LEEQTNKLYA LEINTHPGMM SLSIVPEIAA
310 320
YAGINFTNLI EEIIKTASFE S
Length:321
Mass (Da):35,847
Last modified:November 13, 2007 - v1
Checksum:i4EA3B39683D3BC4C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000848 Genomic DNA. Translation: ABV75946.1.
RefSeqiYP_001494454.1. NC_009882.1.

Genome annotation databases

EnsemblBacteriaiABV75946; ABV75946; A1G_01910.
KEGGirri:A1G_01910.
PATRICi17903467. VBIRicRic5337_0398.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000848 Genomic DNA. Translation: ABV75946.1.
RefSeqiYP_001494454.1. NC_009882.1.

3D structure databases

ProteinModelPortaliA8GRC1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi392021.A1G_01910.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABV75946; ABV75946; A1G_01910.
KEGGirri:A1G_01910.
PATRICi17903467. VBIRicRic5337_0398.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiKYTEGFA.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciRRIC392021:GIY1-359-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.
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. "Complete genome sequence of Rickettsia rickettsii."
    Madan A., Fahey J., Helton E., Ketteman M., Madan A., Rodrigues S., Sanchez A., Dasch G., Eremeeva M.
    Submitted (SEP-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Sheila Smith.

Entry informationi

Entry nameiDDL_RICRS
AccessioniPrimary (citable) accession number: A8GRC1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 13, 2007
Last modified: April 1, 2015
This is version 54 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

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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.