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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Coxiella burnetii (strain Dugway 5J108-111)
Status
Reviewed-Annotation score: Annotation score: 4 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 bindingi303 – 3031Magnesium or manganese 1UniRule annotation
Metal bindingi316 – 3161Magnesium or manganese 1UniRule annotation
Metal bindingi316 – 3161Magnesium or manganese 2UniRule annotation
Metal bindingi318 – 3181Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi176 – 23156ATPUniRule 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

BioCyciCBUR434922:GJTP-1512-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:CBUD_1427
OrganismiCoxiella burnetii (strain Dugway 5J108-111)
Taxonomic identifieri434922 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaLegionellalesCoxiellaceaeCoxiella
ProteomesiUP000008555: Chromosome

Subcellular locationi

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 – 372372D-alanine--D-alanine ligasePRO_1000074771Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi434922.CBUD_1427.

Structurei

3D structure databases

ProteinModelPortaliA9KGD2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini145 – 349205ATP-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.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A9KGD2-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAEKLHISVL CGGQSTEHEI SIQSAKNIVN TLDAAKYLIS VIFIDHVGRW
60 70 80 90 100
YLIDQPEMFL AHSPDHLVKE GSARPITIAF GDAAKPWQSL NGDGRRYSAD
110 120 130 140 150
CVFPMVHGTQ GEDGALQGLL ELLNLPYVGA NVQSSAVCME KDLTKTVLRA
160 170 180 190 200
GGIPVVDWHT LSPRDATEGV YQRLLDRWGT SELFVKAVSL GSSVATLPVK
210 220 230 240 250
TETEFTKAVK EVFRYDDRLM VEPRIRGREI ECAVLGNGAP KASLPGEIIP
260 270 280 290 300
HHDYYSYDAK YLDPNGATTT TSVDLSESVT KQIQQIAIDA FKMVHCSGMA
310 320 330 340 350
RVDFFVTPNN KVLVNEINTI PGFTNISMYP KMWEASGLPC PNLLDQLIEL
360 370
AIDRHQEQQK LIRCYEVKAR SL
Length:372
Mass (Da):41,218
Last modified:February 5, 2008 - v1
Checksum:iC983B28F92B519EC
GO

Sequence cautioni

The sequence ABS77778.2 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000733 Genomic DNA. Translation: ABS77778.2. Different initiation.
RefSeqiYP_001424774.2. NC_009727.1.

Genome annotation databases

EnsemblBacteriaiABS77778; ABS77778; CBUD_1427.
GeneIDi5458117.
KEGGicbd:CBUD_1427.
PATRICi17922661. VBICoxBur32972_1422.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000733 Genomic DNA. Translation: ABS77778.2. Different initiation.
RefSeqiYP_001424774.2. NC_009727.1.

3D structure databases

ProteinModelPortaliA9KGD2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi434922.CBUD_1427.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABS77778; ABS77778; CBUD_1427.
GeneIDi5458117.
KEGGicbd:CBUD_1427.
PATRICi17922661. VBICoxBur32972_1422.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciCBUR434922:GJTP-1512-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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Comparative genomics reveal extensive transposon-mediated genomic plasticity and diversity among potential effector proteins within the genus Coxiella."
    Beare P.A., Unsworth N., Andoh M., Voth D.E., Omsland A., Gilk S.D., Williams K.P., Sobral B.W., Kupko J.J. III, Porcella S.F., Samuel J.E., Heinzen R.A.
    Infect. Immun. 77:642-656(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Dugway 5J108-111.

Entry informationi

Entry nameiDDL_COXBN
AccessioniPrimary (citable) accession number: A9KGD2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: February 5, 2008
Last modified: February 4, 2015
This is version 58 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.