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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber)
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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi271 – 2711Magnesium or manganese 1UniRule annotation
Metal bindingi284 – 2841Magnesium or manganese 1UniRule annotation
Metal bindingi284 – 2841Magnesium or manganese 2UniRule annotation
Metal bindingi286 – 2861Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi146 – 19954ATPUniRule 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

BioCyciMRUB504728:GI6U-342-MONOMER.
UniPathwayiUPA00219.

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 annotationImported
ORF Names:K649_01305Imported
OrganismiMeiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber)Imported
Taxonomic identifieri504728 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeMeiothermus
ProteomesiUP000013026 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

STRINGi504728.Mrub_0337.

Structurei

3D structure databases

ProteinModelPortaliD3PM04.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 317198ATP-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

HOGENOMiHOG000011593.
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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D3PM04-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKVLLLAGGP PGEHEVSLSS ARGVLAAMPH PTELVVIAKD GRWLLGEDAY
60 70 80 90 100
EALRAGVAEQ GTHPFPPPVP WQHYDVVFPL LHGPLGEDGV IQGFLQLLRR
110 120 130 140 150
PYVGAGVASS ALCMDKDLCK RVLRQAGIPV VPWVTLYKGE PTPQPPFPPP
160 170 180 190 200
YFVKPANTGS SVGISKVKAD QDATRALAEA FAWDDKVLVE QGIEGVRELE
210 220 230 240 250
VALLGNIHAE ASVVGEITYQ SEFYDYETKY TEGKAQLHLP APIPPELSDE
260 270 280 290 300
IRATALEAYR ILGVRGMARV DFFLSPQGEL YLNEFNTIPG FTPTSMYPKL
310 320
WQATGLAYPD LLDRLVRLAL ER
Length:322
Mass (Da):35,231
Last modified:April 20, 2010 - v1
Checksum:i396C70BD2892732B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP005385 Genomic DNA. Translation: AGK03569.1.
RefSeqiWP_013012634.1. NC_021081.1.

Genome annotation databases

EnsemblBacteriaiADD27115; ADD27115; Mrub_0337.
AGK03569; AGK03569; K649_01305.
KEGGimrb:Mrub_0337.
mre:K649_01305.
PATRICi35356778. VBIMeiRub128672_0343.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP005385 Genomic DNA. Translation: AGK03569.1.
RefSeqiWP_013012634.1. NC_021081.1.

3D structure databases

ProteinModelPortaliD3PM04.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi504728.Mrub_0337.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADD27115; ADD27115; Mrub_0337.
AGK03569; AGK03569; K649_01305.
KEGGimrb:Mrub_0337.
mre:K649_01305.
PATRICi35356778. VBIMeiRub128672_0343.

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciMRUB504728:GI6U-342-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. Chin J., Alexander D.H., Marks P., Korlach J., Clum A., Copeland A.
    Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: DSM 1279Imported.

Entry informationi

Entry nameiD3PM04_MEIRD
AccessioniPrimary (citable) accession number: D3PM04
Entry historyi
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: July 22, 2015
This is version 48 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.