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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Clostridium saccharolyticum (strain ATCC 35040 / DSM 2544 / NRCC 2533 / WM1)
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 bindingi287 – 2871Magnesium or manganese 1UniRule annotation
Metal bindingi300 – 3001Magnesium or manganese 1UniRule annotation
Metal bindingi300 – 3001Magnesium or manganese 2UniRule annotation
Metal bindingi302 – 3021Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi168 – 21952ATPUniRule 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

BioCyciCSAC610130:GHTP-1304-MONOMER.
UniPathwayiUPA00219.
UPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:Closa_1258Imported
OrganismiClostridium saccharolyticum (strain ATCC 35040 / DSM 2544 / NRCC 2533 / WM1)Imported
Taxonomic identifieri610130 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesLachnospiraceae
ProteomesiUP000001662 Componenti: Chromosome

Subcellular locationi

  1. 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

ProteinModelPortaliD9R8A9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini142 – 333192ATP-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

HOGENOMiHOG000011592.
KOiK01921.
OMAiARYNPGR.

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]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D9R8A9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIVVLAGGF SPEREVSLSS GAMITNALIR TGHEVYLLDS YLGAADGEEV
60 70 80 90 100
RFKSLHDGTG FFWEIGREVP ELDRLSKERN GKGYIGNRVI EICGLADIVF
110 120 130 140 150
VALHGGAGEN GQIQAVLDAY GISYTGTGYE GCLKAMDKPM AKLLMRNSGI
160 170 180 190 200
PTPDWRLYSR GESLEPFPYP CVVKPCGCGS SVGITMVEGE DQWEMALDSA
210 220 230 240 250
FSYEDRVLAE VKITGREFSV GILGERALPA IEIIPKKGFY DYENKYQAGL
260 270 280 290 300
TEEICPASLT EEQEEFMGCM ALKVHRVLGL GYYSRVDFLM EEDGSLFCLE
310 320 330 340 350
ANTLPGMTPF SLLPQKAQAA GISYQELCEE IVSHGIHPAG VPLYPAKREH

S
Length:351
Mass (Da):38,436
Last modified:October 5, 2010 - v1
Checksum:i346E4ECB574B1F4F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002109 Genomic DNA. Translation: ADL03861.1.
RefSeqiWP_013271956.1. NC_014376.1.
YP_003821484.1. NC_014376.1.

Genome annotation databases

EnsemblBacteriaiADL03861; ADL03861; Closa_1258.
KEGGicsh:Closa_1258.
PATRICi42263968. VBICloSac91065_1368.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002109 Genomic DNA. Translation: ADL03861.1.
RefSeqiWP_013271956.1. NC_014376.1.
YP_003821484.1. NC_014376.1.

3D structure databases

ProteinModelPortaliD9R8A9.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADL03861; ADL03861; Closa_1258.
KEGGicsh:Closa_1258.
PATRICi42263968. VBICloSac91065_1368.

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiARYNPGR.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciCSAC610130:GHTP-1304-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]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 35040 / DSM 2544 / NRCC 2533 / WM1Imported.

Entry informationi

Entry nameiD9R8A9_CLOSW
AccessioniPrimary (citable) accession number: D9R8A9
Entry historyi
Integrated into UniProtKB/TrEMBL: October 5, 2010
Last sequence update: October 5, 2010
Last modified: April 29, 2015
This is version 33 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.