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Q163J4

- DDL_ROSDO

UniProt

Q163J4 - DDL_ROSDO

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Protein
D-alanine--D-alanine ligase
Gene
ddl, RD1_3351
Organism
Roseobacter denitrificans (strain ATCC 33942 / OCh 114) (Erythrobacter sp. (strain OCh 114)) (Roseobacter denitrificans)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.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 bindingi264 – 2641Magnesium or manganese 1 By similarity
Metal bindingi280 – 2801Magnesium or manganese 1 By similarity
Metal bindingi280 – 2801Magnesium or manganese 2 By similarity
Metal bindingi282 – 2821Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi147 – 19751ATP By similarity
Add
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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciRDEN375451:GJIZ-3159-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:RD1_3351
OrganismiRoseobacter denitrificans (strain ATCC 33942 / OCh 114) (Erythrobacter sp. (strain OCh 114)) (Roseobacter denitrificans)
Taxonomic identifieri375451 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeRoseobacter
ProteomesiUP000007029: Chromosome

Subcellular locationi

Cytoplasm By similarity 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 – 319319D-alanine--D-alanine ligaseUniRule annotation
PRO_0000341170Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi375451.RD1_3351.

Structurei

3D structure databases

ProteinModelPortaliQ163J4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 313194ATP-grasp
Add
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
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.

Q163J4-1 [UniParc]FASTAAdd to Basket

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MTGPEWAHTR GTKVGQSSRT PPKVAVLLGG PSVEREVSLS SGQACAAALR    50
DEGYDVVEID AGHDLGARLI DAGPDAVLNC LHGRWGEDGC VQGLLEWMGV 100
PYSHSGVLAS ALAMDKQRSK DAFVAAGLPV VPSVIAKAAD VRMGHVMQPP 150
YVVKPNNEGS SVGVYLVHEA ANGPPQLSED MPQEVMVEAF APGRELTTTV 200
VGDRALTVTD IVTDGWYDYD AKYKPGGSHH VVPADIPADI FDLCMDYALR 250
AHHALGCRGV SRTDFRWDET KGAAGLILLE TNTQPGMTAT SLTPEQAAVT 300
GMTFGKLCAW MVEDASCDR 319
Length:319
Mass (Da):33,854
Last modified:June 10, 2008 - v2
Checksum:i44CB158B7DB87894
GO

Sequence cautioni

The sequence ABG32849.1 differs from that shown. Reason: Erroneous initiation.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000362 Genomic DNA. Translation: ABG32849.1. Different initiation.
RefSeqiYP_683535.1. NC_008209.1.

Genome annotation databases

EnsemblBacteriaiABG32849; ABG32849; RD1_3351.
GeneIDi4195054.
KEGGirde:RD1_3351.
PATRICi23364663. VBIRosDen86677_3201.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000362 Genomic DNA. Translation: ABG32849.1 . Different initiation.
RefSeqi YP_683535.1. NC_008209.1.

3D structure databases

ProteinModelPortali Q163J4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 375451.RD1_3351.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABG32849 ; ABG32849 ; RD1_3351 .
GeneIDi 4195054.
KEGGi rde:RD1_3351.
PATRICi 23364663. VBIRosDen86677_3201.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci RDEN375451:GJIZ-3159-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: ATCC 33942 / OCh 114.

Entry informationi

Entry nameiDDL_ROSDO
AccessioniPrimary (citable) accession number: Q163J4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 10, 2008
Last modified: May 14, 2014
This is version 62 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

Documents

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

External Data

Dasty 3

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