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Protein

D-alanine--D-alanine ligase

Gene

ddlB

Organism
Clavibacter michiganensis subsp. michiganensis (strain NCPPB 382)
Status
Unreviewed-Annotation score: Annotation score: 4 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

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation
  • Mg2+, Mn2+Note: Binds 2 magnesium or manganese ions per subunit.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi266 – 2661Magnesium or manganese 1UniRule annotation
Metal bindingi279 – 2791Magnesium or manganese 1UniRule annotation
Metal bindingi279 – 2791Magnesium or manganese 2UniRule annotation
Metal bindingi281 – 2811Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi139 – 19456ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

BioCyciCMIC443906:GCI2-3059-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:ddlBImported
Synonyms:ddlUniRule annotation
Ordered Locus Names:CMM_2970Imported
OrganismiClavibacter michiganensis subsp. michiganensis (strain NCPPB 382)Imported
Taxonomic identifieri443906 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesMicrococcineaeMicrobacteriaceaeClavibacter
ProteomesiUP000001564 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi443906.CMM_2970.

Structurei

3D structure databases

ProteinModelPortaliA5CVB8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini105 – 312208ATP-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.
OMAiEICPGRF.
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.
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.
PROSITEiPS50975. ATP_GRASP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A5CVB8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTAHEPLSVL VLAGGISHER DVSLRSGRRV ADALRAAGVQ ASLRDPDATL
60 70 80 90 100
LDFLRDTPPA VVWPVLHGAS GEDGALLGLL ELAGVPYVGS SARSARLAWD
110 120 130 140 150
KPTAKAIAES AGIRTPRSVT LPKDTFRELG AAAVLRLVTE AVPAPYAVKP
160 170 180 190 200
ARGGSAQGVT IVTDAEALPR AMVDAYTYGD VALIEQLVEG TEVAIGILDT
210 220 230 240 250
GDGPEALPAT EIVPTSGVYG YEARYNAGLT RFFTPARISP DANAAASAAA
260 270 280 290 300
IGIHRALGIG QMSRVDIIID AAGEPWFIEV NVIPGLTETS LLPQGLAAAG
310 320
VEVGDLYRRL AEAARGASSG P
Length:321
Mass (Da):33,111
Last modified:June 12, 2007 - v1
Checksum:i9164F5CB177CB585
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM711867 Genomic DNA. Translation: CAN03057.1.
RefSeqiWP_012039657.1. NC_009480.1.
YP_001223715.1. NC_009480.1.

Genome annotation databases

EnsemblBacteriaiCAN03057; CAN03057; CMM_2970.
KEGGicmi:CMM_2970.
PATRICi21456815. VBIClaMic82482_3100.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM711867 Genomic DNA. Translation: CAN03057.1.
RefSeqiWP_012039657.1. NC_009480.1.
YP_001223715.1. NC_009480.1.

3D structure databases

ProteinModelPortaliA5CVB8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi443906.CMM_2970.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAN03057; CAN03057; CMM_2970.
KEGGicmi:CMM_2970.
PATRICi21456815. VBIClaMic82482_3100.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiEICPGRF.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciCMIC443906:GCI2-3059-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.
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.
PROSITEiPS50975. ATP_GRASP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity."
    Gartemann K.H., Abt B., Bekel T., Burger A., Engemann J., Flugel M., Gaigalat L., Goesmann A., Grafen I., Kalinowski J., Kaup O., Kirchner O., Krause L., Linke B., McHardy A., Meyer F., Pohle S., Ruckert C.
    , Schneiker S., Zellermann E.M., Puhler A., Eichenlaub R., Kaiser O., Bartels D.
    J. Bacteriol. 190:2138-2149(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NCPPB 382Imported.

Entry informationi

Entry nameiA5CVB8_CLAM3
AccessioniPrimary (citable) accession number: A5CVB8
Entry historyi
Integrated into UniProtKB/TrEMBL: June 12, 2007
Last sequence update: June 12, 2007
Last modified: May 27, 2015
This is version 62 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete 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.