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B1KV16

- DDL_CLOBM

UniProt

B1KV16 - DDL_CLOBM

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Protein
D-alanine--D-alanine ligase
Gene
ddl, CLK_3656
Organism
Clostridium botulinum (strain Loch Maree / Type A3)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.UniRule annotation

Catalytic activityi

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

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi248 – 2481Magnesium or manganese 1 By similarity
Metal bindingi260 – 2601Magnesium or manganese 1 By similarity
Metal bindingi260 – 2601Magnesium or manganese 2 By similarity
Metal bindingi262 – 2621Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi126 – 18156ATP By similarity
Add
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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciCBOT498214:GH05-504-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:CLK_3656
OrganismiClostridium botulinum (strain Loch Maree / Type A3)
Taxonomic identifieri498214 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium
ProteomesiUP000000722: Chromosome

Subcellular locationi

Cytoplasm By similarity 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 – 300300D-alanine--D-alanine ligaseUniRule annotation
PRO_1000091176Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi498214.CLK_3656.

Structurei

3D structure databases

ProteinModelPortaliB1KV16.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini99 – 293195ATP-grasp
Add
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiDRIQAND.
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. 2 hits.
[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.

B1KV16-1 [UniParc]FASTAAdd to Basket

« Hide

MKIGVIMGGI STEREVSLNS GREVIKYLEL LEHEIIPIII DKKEDVMEKA    50
KGIDFAFLAL HGKFGEDGTV QSVLQTLDIP YSGCGPLTSA ICMDKDMTKK 100
ILKYANINTA DWVNVTNAED IDYEAIEKIG YPVFVKPNSG GSSVATNLVK 150
NKEGIKEAVE LALKYDKEVM IENYTKGEEI TCCMLNGKML PVLAIRPHAE 200
FFDYTAKYAD GGSDEVVIEL EENLHKKVEE MALACWKELK CEVYVRVDMI 250
VKEGVPYVLE LNTLPGMTKN SLFPKSANAV GISFAELLNS IVKYSLEVER 300
Length:300
Mass (Da):33,362
Last modified:April 29, 2008 - v1
Checksum:iB02B7E37A3A77CBF
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000962 Genomic DNA. Translation: ACA56780.1.
RefSeqiWP_012344602.1. NC_010520.1.
YP_001785794.1. NC_010520.1.

Genome annotation databases

EnsemblBacteriaiACA56780; ACA56780; CLK_3656.
GeneIDi6153609.
KEGGicbl:CLK_3656.
PATRICi19386319. VBICloBot822_0774.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000962 Genomic DNA. Translation: ACA56780.1 .
RefSeqi WP_012344602.1. NC_010520.1.
YP_001785794.1. NC_010520.1.

3D structure databases

ProteinModelPortali B1KV16.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 498214.CLK_3656.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACA56780 ; ACA56780 ; CLK_3656 .
GeneIDi 6153609.
KEGGi cbl:CLK_3656.
PATRICi 19386319. VBICloBot822_0774.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011592.
KOi K01921.
OMAi DRIQAND.
OrthoDBi EOG6ND0KB.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci CBOT498214:GH05-504-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Analysis of the neurotoxin complex genes in Clostridium botulinum A1-A4 and B1 strains: BoNT/A3, /Ba4 and /B1 clusters are located within plasmids."
    Smith T.J., Hill K.K., Foley B.T., Detter J.C., Munk A.C., Bruce D.C., Doggett N.A., Smith L.A., Marks J.D., Xie G., Brettin T.S.
    PLoS ONE 2:E1271-E1271(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Loch Maree / Type A3.

Entry informationi

Entry nameiDDL_CLOBM
AccessioniPrimary (citable) accession number: B1KV16
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: April 29, 2008
Last modified: September 3, 2014
This is version 49 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

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