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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Sulfurimonas denitrificans (strain ATCC 33889 / DSM 1251) (Thiomicrospira denitrificans (strain ATCC 33889 / DSM 1251))
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 bindingi284 – 2841Magnesium or manganese 1UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 1UniRule annotation
Metal bindingi296 – 2961Magnesium or manganese 2UniRule annotation
Metal bindingi298 – 2981Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi160 – 21152ATPUniRule 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

BioCyciSDEN326298:GH9P-1256-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:Suden_1208
OrganismiSulfurimonas denitrificans (strain ATCC 33889 / DSM 1251) (Thiomicrospira denitrificans (strain ATCC 33889 / DSM 1251))
Taxonomic identifieri326298 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeSulfurimonas
ProteomesiUP000002714: 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 – 345345D-alanine--D-alanine ligasePRO_0000341179Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi326298.Suden_1208.

Structurei

3D structure databases

ProteinModelPortaliQ30R95.
SMRiQ30R95. Positions 1-324.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini133 – 332200ATP-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.
HOGENOMiHOG000102494.
KOiK01921.
OMAiYRIAFIG.
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. 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.

Q30R95-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLTILFGGA SFEHEISIVS AITLKEKLSN FELNFIFCDQ DHTFYLINAS
60 70 80 90 100
KMRATTFSRG EYKKMPKLTL SHGSFVQKSL FGSVDISGTV LNLIHGGDGE
110 120 130 140 150
DGTIAAILDF FSIKYIGPRV DASVFSYDKR YTKWLCHARG VKCVESQELS
160 170 180 190 200
SSEHSNIKIA YPIIVKPSRL GSSIGVSIVK DESKLDYALD SAFEFDNTVI
210 220 230 240 250
VEPFLEGVKE YNLAGFSAGK KFYFSIIEEP QKEEFLDFEK KYMDFSRSGN
260 270 280 290 300
VDSAEISKEL ESKLRASFEK VYKNLFEGAL IRCDFFVVNG EVFLNEINPI
310 320 330 340
PGSMANYLFD DFGGSLKLLA NSLPHTKRAK VTYEYIHSIS KAKGK
Length:345
Mass (Da):38,726
Last modified:December 6, 2005 - v1
Checksum:iA98030DFD74AF478
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000153 Genomic DNA. Translation: ABB44486.1.
RefSeqiWP_011372838.1. NC_007575.1.
YP_393721.1. NC_007575.1.

Genome annotation databases

EnsemblBacteriaiABB44486; ABB44486; Suden_1208.
GeneIDi3763570.
KEGGitdn:Suden_1208.
PATRICi23771040. VBISulDen68967_1255.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000153 Genomic DNA. Translation: ABB44486.1.
RefSeqiWP_011372838.1. NC_007575.1.
YP_393721.1. NC_007575.1.

3D structure databases

ProteinModelPortaliQ30R95.
SMRiQ30R95. Positions 1-324.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi326298.Suden_1208.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB44486; ABB44486; Suden_1208.
GeneIDi3763570.
KEGGitdn:Suden_1208.
PATRICi23771040. VBISulDen68967_1255.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000102494.
KOiK01921.
OMAiYRIAFIG.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciSDEN326298:GH9P-1256-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33889 / DSM 1251.

Entry informationi

Entry nameiDDL_SULDN
AccessioniPrimary (citable) accession number: Q30R95
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: December 6, 2005
Last modified: March 4, 2015
This is version 75 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, 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

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.