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Q8UDN3

- DDL_AGRT5

UniProt

Q8UDN3 - DDL_AGRT5

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Agrobacterium tumefaciens (strain C58 / ATCC 33970)
Status
Reviewed - 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

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi252 – 2521Magnesium or manganese 1UniRule annotation
Metal bindingi269 – 2691Magnesium or manganese 1UniRule annotation
Metal bindingi269 – 2691Magnesium or manganese 2UniRule annotation
Metal bindingi271 – 2711Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi128 – 18356ATPUniRule 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

BioCyciAGRO:ATU2089-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:Atu2089
ORF Names:AGR_C_3788
OrganismiAgrobacterium tumefaciens (strain C58 / ATCC 33970)
Taxonomic identifieri176299 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
ProteomesiUP000000813: Chromosome circular

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 308308D-alanine--D-alanine ligasePRO_0000177777Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi176299.Atu2089.

Structurei

3D structure databases

ProteinModelPortaliQ8UDN3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini102 – 302201ATP-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.
OMAiLCRWIVE.
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.

Q8UDN3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGGKHVAVLL GGFSSERPVS LSSGNACALA LEGEGYKVTR VDVGRDVAAV
60 70 80 90 100
LDELRPDVAF NALHGPFGED GTIQGILEYL AIPYTHSGVL ASALAMDKAQ
110 120 130 140 150
AKKVAAAAGI PVAGERVMNR FDFTSEHPLQ PPYVVKPVRE GSSFGVVIVK
160 170 180 190 200
EDQSHPPQIL TSSEWPFGNQ VMVERYIHGR ELTCGVLDGE ALGVTEVVPL
210 220 230 240 250
GHNFYDYDAK YAAGGSKHVI PAGISPKIYQ KIQTLAVMAH QAIGCRGVSR
260 270 280 290 300
SDFRYDDRFS EDGEVIWLEV NTQPGMTPTS LVPEMAAHAG RSFGDLVSWM

VEDASCLR
Length:308
Mass (Da):33,069
Last modified:August 2, 2002 - v2
Checksum:i18A95347199404E8
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE007869 Genomic DNA. Translation: AAK87839.2.
PIRiAB2833.
F97610.
RefSeqiNP_355054.2. NC_003062.2.

Genome annotation databases

EnsemblBacteriaiAAK87839; AAK87839; Atu2089.
GeneIDi1134127.
KEGGiatu:Atu2089.
PATRICi20813963. VBIAgrTum91616_2102.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE007869 Genomic DNA. Translation: AAK87839.2 .
PIRi AB2833.
F97610.
RefSeqi NP_355054.2. NC_003062.2.

3D structure databases

ProteinModelPortali Q8UDN3.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 176299.Atu2089.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAK87839 ; AAK87839 ; Atu2089 .
GeneIDi 1134127.
KEGGi atu:Atu2089.
PATRICi 20813963. VBIAgrTum91616_2102.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011592.
KOi K01921.
OMAi LCRWIVE.
OrthoDBi EOG6ND0KB.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci AGRO:ATU2089-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C58 / ATCC 33970.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C58 / ATCC 33970.

Entry informationi

Entry nameiDDL_AGRT5
AccessioniPrimary (citable) accession number: Q8UDN3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: August 2, 2002
Last modified: October 29, 2014
This is version 88 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3