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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
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: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation
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)DescriptionActionsGraphical viewLength
Metal bindingi268Magnesium or manganese 1UniRule annotation1
Metal bindingi282Magnesium or manganese 1UniRule annotation1
Metal bindingi282Magnesium or manganese 2UniRule annotation1
Metal bindingi284Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi147 – 199ATPUniRule annotationAdd BLAST53

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

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:RF_1035
OrganismiRickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
Taxonomic identifieri315456 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiaspotted fever group
Proteomesi
  • UP000008548 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002779181 – 321D-alanine--D-alanine ligaseAdd BLAST321

Interactioni

Protein-protein interaction databases

STRINGi315456.RF_1035.

Structurei

3D structure databases

ProteinModelPortaliQ4UKP1.
SMRiQ4UKP1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini121 – 315ATP-graspUniRule annotationAdd BLAST195

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiYETKYTE.
OrthoDBiPOG091H00GT.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiView protein in InterPro
IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
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.
PfamiView protein in Pfam
PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiView protein in PROSITE
PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.

Sequencei

Sequence statusi: Complete.

Q4UKP1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKYQTHWVE HSEVKILSTT GKKHIALVAG GMSAEREVSL VSSEGVSKAL
60 70 80 90 100
IELGYKVTFI DMGADIAVKL QEIKPDIVFN CLHGTYGEDG CLPGLLNIMR
110 120 130 140 150
IPYTHSGVLS SALAFDKIHS RSWFLTNNIN MAESIIVNKS DNIKSDPVKR
160 170 180 190 200
PYVIKPLTQG SSIGVEVIFE EDDFNFADYN FPYGYQVIIE QYIKGRELQV
210 220 230 240 250
AVLNGKALGA LEIKLLKNRF YDYETKYTEG FAEHLCPAPL PTNLYEKLLV
260 270 280 290 300
ESEKIYKTMN CKGPARAEFI LEEQTNKLYA LEINTHPGMT PLSIVPEIAA
310 320
YAGINFTNLI EEIIKTASFE S
Length:321
Mass (Da):35,914
Last modified:July 5, 2005 - v1
Checksum:i6F91460A67161BE8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000053 Genomic DNA. Translation: AAY61886.1.
RefSeqiWP_011271351.1. NC_007109.1.

Genome annotation databases

EnsemblBacteriaiAAY61886; AAY61886; RF_1035.
KEGGirfe:RF_1035.

Similar proteinsi

Entry informationi

Entry nameiDDL_RICFE
AccessioniPrimary (citable) accession number: Q4UKP1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 20, 2007
Last sequence update: July 5, 2005
Last modified: August 30, 2017
This is version 89 of the entry and version 1 of the sequence. See 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. Rickettsia felis (Rickettsia azadi)
    Rickettsia felis (strain URRWXCal2): entries and gene names
  3. SIMILARITY comments
    Index of protein domains and families