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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Staphylococcus aureus (strain JH1)
Status
Reviewed-Annotation score: 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

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 bindingi293 – 2931Magnesium or manganese 1UniRule annotation
Metal bindingi306 – 3061Magnesium or manganese 1UniRule annotation
Metal bindingi306 – 3061Magnesium or manganese 2UniRule annotation
Metal bindingi308 – 3081Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi167 – 22256ATPUniRule 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

BioCyciSAUR359787:GCG4-2227-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:SaurJH1_2158
OrganismiStaphylococcus aureus (strain JH1)
Taxonomic identifieri359787 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcus
ProteomesiUP000001109: 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 – 356356D-alanine--D-alanine ligasePRO_1000074797Add
BLAST

Proteomic databases

PRIDEiA6U3G9.

Interactioni

Protein-protein interaction databases

STRINGi359787.SaurJH1_2158.

Structurei

3D structure databases

ProteinModelPortaliA6U3G9.
SMRiA6U3G9. Positions 3-356.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini134 – 339206ATP-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.

A6U3G9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKENICIVF GGKSAEHEVS ILTAQNVLNA IDKDKYHVDI IYITNDGDWR
60 70 80 90 100
KQNNITAEIK STDELHLENG EALEISQLLK ESSSGQPYDA VFPLLHGPNG
110 120 130 140 150
EDGTIQGLFE VLDVPYVGNG VLSAASSMDK LVMKQLFEHR GLPQLPYISF
160 170 180 190 200
LRSEYEKYEH NILKLVNDKL NYPVFVKPAN LGSSVGISKC NNEAELKEGI
210 220 230 240 250
KEAFQFDRKL VIEQGVNARE IEVAVLGNDY PEATWPGEVV KDVAFYDYKS
260 270 280 290 300
KYKDGKVQLQ IPADLDEDVQ LTLRNMALEA FKATDCSGLV RADFFVTEDN
310 320 330 340 350
QIYINETNAM PGFTAFSMYP KLWENMGLSY PELITKLIEL AKERHQDKQK

NKYKID
Length:356
Mass (Da):40,231
Last modified:August 21, 2007 - v1
Checksum:i65822883958DC645
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000736 Genomic DNA. Translation: ABR52987.1.
RefSeqiYP_001317274.1. NC_009632.1.

Genome annotation databases

EnsemblBacteriaiABR52987; ABR52987; SaurJH1_2158.
GeneIDi5317202.
KEGGisah:SaurJH1_2158.
PATRICi19536276. VBIStaAur98826_2205.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000736 Genomic DNA. Translation: ABR52987.1.
RefSeqiYP_001317274.1. NC_009632.1.

3D structure databases

ProteinModelPortaliA6U3G9.
SMRiA6U3G9. Positions 3-356.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi359787.SaurJH1_2158.

Proteomic databases

PRIDEiA6U3G9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR52987; ABR52987; SaurJH1_2158.
GeneIDi5317202.
KEGGisah:SaurJH1_2158.
PATRICi19536276. VBIStaAur98826_2205.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciSAUR359787:GCG4-2227-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. "Complete sequence of chromosome of Staphylococcus aureus subsp. aureus JH1."
    US DOE Joint Genome Institute
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.
    , Hauser L., Kyrpides N., Ivanova N., Tomasz A., Richardson P.
    Submitted (JUN-2007) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JH1.

Entry informationi

Entry nameiDDL_STAA2
AccessioniPrimary (citable) accession number: A6U3G9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: August 21, 2007
Last modified: January 7, 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.