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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Melissococcus plutonius (strain DAT561)
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

Pathway:ipeptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotationSAAS annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Pathway:ipeptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi295 – 2951Magnesium or manganese 1UniRule annotation
Metal bindingi308 – 3081Magnesium or manganese 1UniRule annotation
Metal bindingi308 – 3081Magnesium or manganese 2UniRule annotation
Metal bindingi310 – 3101Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi169 – 22456ATPUniRule 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

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:MPD5_0408Imported
OrganismiMelissococcus plutonius (strain DAT561)Imported
Taxonomic identifieri1090974 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeMelissococcus
ProteomesiUP000009055 Componenti: Chromosome 1

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini136 – 341206ATP-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

KOiK01921.
OMAiMDKIAMK.

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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

H5T3E0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIILLYGGK SEEHDVSILS AYSILNAIYY EYYTVQLVLI TKQGEWIKGP
60 70 80 90 100
LLTEKPENKE ILNLTGAKDE NTMAYSSGTS IMPCEIFEKD AIVFPVLHGP
110 120 130 140 150
NGEDGTIQGF LETIGMPYVG TGVLASATAM DKIMTKYLLQ TVGIPQTPYV
160 170 180 190 200
PVLKNEWKND SKQLFERCEG TLLYPMFVKP ANLGSSVGIS KVENREELQK
210 220 230 240 250
ALELAYKYDS RVIVEQGIEA REIEVAILGN EDVRTTLPGE VVKNVDFYDY
260 270 280 290 300
QAKYVDNQIS MQIPAELPAE VCRQAQEYAK KAYKTLDGSG LSRCDFFLTN
310 320 330 340 350
KNELFLNELN TMPGFTEFSM YPSLWENMGL KYSDLIEELI QLGLNRFEQR

QRFFNN
Length:356
Mass (Da):40,335
Last modified:April 18, 2012 - v1
Checksum:i4197403A4785345A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP012282 Genomic DNA. Translation: BAL61683.1.
RefSeqiWP_015694609.1. NC_016938.1.

Genome annotation databases

EnsemblBacteriaiBAL61683; BAL61683; MPD5_0408.
KEGGimpx:MPD5_0408.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP012282 Genomic DNA. Translation: BAL61683.1.
RefSeqiWP_015694609.1. NC_016938.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAL61683; BAL61683; MPD5_0408.
KEGGimpx:MPD5_0408.

Phylogenomic databases

KOiK01921.
OMAiMDKIAMK.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.

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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of Melissococcus plutonius DAT561, a strain that shows an unusual growth profile and is representative of an endemic cluster in Japan."
    Okumura K., Arai R., Okura M., Kirikae T., Takamatsu D., Osaki M., Miyoshi-Akiyama T.
    J. Bacteriol. 194:3014-3014(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DAT561Imported.

Entry informationi

Entry nameiH5T3E0_MELPD
AccessioniPrimary (citable) accession number: H5T3E0
Entry historyi
Integrated into UniProtKB/TrEMBL: April 18, 2012
Last sequence update: April 18, 2012
Last modified: July 22, 2015
This is version 28 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.