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B9E560

- DDL_CLOK1

UniProt

B9E560 - DDL_CLOK1

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Clostridium kluyveri (strain NBRC 12016)
Status
Reviewed - 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

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi249 – 2491Magnesium or manganese 1UniRule annotation
Metal bindingi261 – 2611Magnesium or manganese 1UniRule annotation
Metal bindingi261 – 2611Magnesium or manganese 2UniRule annotation
Metal bindingi263 – 2631Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi126 – 18156ATPUniRule 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

BioCyciCKLU583346:GJNQ-2630-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:CKR_2584
OrganismiClostridium kluyveri (strain NBRC 12016)
Taxonomic identifieri583346 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesClostridiaceaeClostridium
ProteomesiUP000007969: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 297297D-alanine--D-alanine ligasePRO_1000189733Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi583346.CKR_2584.

Structurei

3D structure databases

ProteinModelPortaliB9E560.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini99 – 294196ATP-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.
HOGENOMiHOG000011592.
KOiK01921.
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.

B9E560-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKVGIIMGGI SSEREVSLNS GKSIINYMDK NKYEIVPIVI DKKNDVFEKV
60 70 80 90 100
KDIDFAFIAL HGKFGEDGII QSVFQTMDIP YSGCSPLTSG ICMDKDISKK
110 120 130 140 150
LLYSANINTA EWICIKSIEN IDYDYLEKMG YPVVVKPNSG GSSVATTIIE
160 170 180 190 200
KSEDIEEAAR LAFNYDEEVM IEKYIEGDEI TCCILDGTAL PILAIKPNKG
210 220 230 240 250
SFFDYTSKYA DGGSEEIVVE FEKPLQSKIE EISLKCWELF KCKGYVRVDM
260 270 280 290
ILKDKVPYVL ELNTLPGLTK NSLFPKSANG VNISFTELLD KIIQCSM
Length:297
Mass (Da):33,188
Last modified:March 24, 2009 - v1
Checksum:iC4647A650D1B5B75
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP009049 Genomic DNA. Translation: BAH07635.1.
RefSeqiWP_012103258.1. NC_011837.1.
YP_002473049.1. NC_011837.1.

Genome annotation databases

EnsemblBacteriaiBAH07635; BAH07635; CKR_2584.
GeneIDi7273001.
KEGGickr:CKR_2584.
PATRICi19475344. VBICloKlu118830_2918.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP009049 Genomic DNA. Translation: BAH07635.1 .
RefSeqi WP_012103258.1. NC_011837.1.
YP_002473049.1. NC_011837.1.

3D structure databases

ProteinModelPortali B9E560.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 583346.CKR_2584.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAH07635 ; BAH07635 ; CKR_2584 .
GeneIDi 7273001.
KEGGi ckr:CKR_2584.
PATRICi 19475344. VBICloKlu118830_2918.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci CKLU583346:GJNQ-2630-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. "Complete genome sequence of Clostridium kluyveri and comparative genomics of Clostridia species."
    Inui M., Nonaka H., Shinoda Y., Ikenaga Y., Abe M., Naito K., Vertes A.A., Yukawa H.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NBRC 12016.

Entry informationi

Entry nameiDDL_CLOK1
AccessioniPrimary (citable) accession number: B9E560
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 28, 2009
Last sequence update: March 24, 2009
Last modified: October 29, 2014
This is version 41 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