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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)
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 bindingi288 – 2881Magnesium or manganese 1UniRule annotation
Metal bindingi301 – 3011Magnesium or manganese 1UniRule annotation
Metal bindingi301 – 3011Magnesium or manganese 2UniRule annotation
Metal bindingi303 – 3031Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi162 – 21756ATPUniRule 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

BioCyciSPYO198466:GJDL-1146-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
Synonyms:ddlA
Ordered Locus Names:SpyM3_1084
OrganismiStreptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)
Taxonomic identifieri198466 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
ProteomesiUP000000564: 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 – 348348D-alanine--D-alanine ligasePRO_0000177890Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliP0DA50.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini132 – 334203ATP-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

HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

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. 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.

P0DA50-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKQTLVLLY GGRSAEREVS VLSAESVMRA VNYDKFLVKT YFITQMGQFI
60 70 80 90 100
KTQQFSEKPS ESERLMTNET IELTQKIKPS DIYEEGAVVF PVLHGPMGED
110 120 130 140 150
GSIQGFLEVL RMPYIGTNVM SSSIAMDKIT TKRVLESIGI PQVAYTVYID
160 170 180 190 200
GQDLEACLVE TLARLTFPIF VKPANMGSSV GISKAQTKVE LRKAIQLALT
210 220 230 240 250
YDSRVLIEQG VVAREIEVGL LGNDKVKSTL PGEVIKDVDF YDYQAKYVDN
260 270 280 290 300
KITMAIPADV DQSIVTEMRS YAEVAFKALG GCGLSRCDFF LTQDGQVYLN
310 320 330 340
ELNTMPGFTQ WSMYPLLWEN MGLAYPDLIE ELVTLAQEIF DQRESHLI
Length:348
Mass (Da):38,951
Last modified:July 27, 2011 - v1
Checksum:iBC270B78EBD31314
GO

Sequence cautioni

The sequence AAM79691.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014074 Genomic DNA. Translation: AAM79691.1. Different initiation.
RefSeqiNP_664888.1. NC_004070.1.

Genome annotation databases

EnsemblBacteriaiAAM79691; AAM79691; SpyM3_1084.
GeneIDi1009399.
KEGGispg:SpyM3_1084.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014074 Genomic DNA. Translation: AAM79691.1. Different initiation.
RefSeqiNP_664888.1. NC_004070.1.

3D structure databases

ProteinModelPortaliP0DA50.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM79691; AAM79691; SpyM3_1084.
GeneIDi1009399.
KEGGispg:SpyM3_1084.

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciSPYO198466:GJDL-1146-MONOMER.

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. 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. "Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence."
    Beres S.B., Sylva G.L., Barbian K.D., Lei B., Hoff J.S., Mammarella N.D., Liu M.-Y., Smoot J.C., Porcella S.F., Parkins L.D., Campbell D.S., Smith T.M., McCormick J.K., Leung D.Y.M., Schlievert P.M., Musser J.M.
    Proc. Natl. Acad. Sci. U.S.A. 99:10078-10083(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-595 / MGAS315.

Entry informationi

Entry nameiDDL_STRP3
AccessioniPrimary (citable) accession number: P0DA50
Secondary accession number(s): Q878Y1, Q8K6X7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 27, 2011
Last sequence update: July 27, 2011
Last modified: January 7, 2015
This is version 23 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.