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Protein
Submitted name:

D-alanine--D-alanine ligase

Gene

ddlA

Organism
Amycolatopsis mediterranei (strain S699) (Nocardia mediterranei)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotationSAAS annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi263 – 2631Magnesium or manganese 1UniRule annotation
Metal bindingi276 – 2761Magnesium or manganese 1UniRule annotation
Metal bindingi276 – 2761Magnesium or manganese 2UniRule annotation
Metal bindingi278 – 2781Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi136 – 19156ATPUniRule 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

LigaseUniRule annotationSAAS annotation

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotation, Peptidoglycan synthesisUniRule annotationSAAS annotation

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, ManganeseUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Submitted name:
D-alanine--D-alanine ligaseImported
Submitted name:
D-alanine-D-alanine ligaseImported
Gene namesi
Name:ddlAImported
Synonyms:ddlUniRule annotation
Ordered Locus Names:AMES_9219Imported, RAM_47985Imported
OrganismiAmycolatopsis mediterranei (strain S699) (Nocardia mediterranei)Imported
Taxonomic identifieri713604 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesPseudonocardineaePseudonocardiaceaeAmycolatopsis
ProteomesiUP000006138 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Structurei

3D structure databases

ProteinModelPortaliG0G1G3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini102 – 309208ATP-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

KOiK01921.

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.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

G0G1G3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDRTVAVLA GGLSHERDVS LRSGRRLSAA LKSESFGIEE WDTDAGLLER
60 70 80 90 100
LRTQRPDAVV VALHGGEGEN GSVQTVLEML GVPFVGTGSQ GCRRAWDKPT
110 120 130 140 150
AKALVQNAGF VTPGWVVLPH STFRELGAQA VLDAMVETLG LPLILKPDQG
160 170 180 190 200
GSALGTQVVR EAAELPAAMV GCFAYGDTVL AERFVDGVEV AVTVIEGEDG
210 220 230 240 250
PEALPAVEIV PESGVYDYTA RYTAGLTDFF TPARLDDAAA KAVAELAVAA
260 270 280 290 300
HRVLGLRDIS RTDAVVMADG TVHFLEVNPS PGLTETSTVP MAIEAAGKSL
310
GAVFGELIGR AISR
Length:314
Mass (Da):32,874
Last modified:October 18, 2011 - v1
Checksum:iA6FD5F392EC6E661
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002896 Genomic DNA. Translation: AEK48062.1.
CP003729 Genomic DNA. Translation: AFO82751.1.
RefSeqiYP_005537519.1. NC_017186.1.
YP_006555696.1. NC_018266.1.

Genome annotation databases

EnsemblBacteriaiAEK48062; AEK48062; RAM_47985.
AFO82751; AFO82751; AMES_9219.
KEGGiamm:AMES_9219.
amn:RAM_47985.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002896 Genomic DNA. Translation: AEK48062.1.
CP003729 Genomic DNA. Translation: AFO82751.1.
RefSeqiYP_005537519.1. NC_017186.1.
YP_006555696.1. NC_018266.1.

3D structure databases

ProteinModelPortaliG0G1G3.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEK48062; AEK48062; RAM_47985.
AFO82751; AFO82751; AMES_9219.
KEGGiamm:AMES_9219.
amn:RAM_47985.

Phylogenomic databases

KOiK01921.

Enzyme and pathway databases

UniPathwayiUPA00219.

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.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Whole genome sequence of the rifamycin B-producing strain Amycolatopsis mediterranei S699."
    Verma M., Kaur J., Kumar M., Kumari K., Saxena A., Anand S., Nigam A., Ravi V., Raghuvanshi S., Khurana P., Tyagi A.K., Khurana J.P., Lal R.
    J. Bacteriol. 193:5562-5563(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S699Imported.
  2. "Complete genome sequence of Amycolatopsis mediterranei S699 based on de novo assembly via a combinatorial sequencing strategy."
    Tang B., Zhao W., Zheng H., Zhuo Y., Zhang L., Zhao G.P.
    J. Bacteriol. 194:5699-5700(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: S699Imported.
  3. Biao T.
    Submitted (JUN-2012) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: S699Imported.

Entry informationi

Entry nameiG0G1G3_AMYMS
AccessioniPrimary (citable) accession number: G0G1G3
Entry historyi
Integrated into UniProtKB/TrEMBL: October 18, 2011
Last sequence update: October 18, 2011
Last modified: March 31, 2015
This is version 31 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.