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D3PM04

- D3PM04_MEIRD

UniProt

D3PM04 - D3PM04_MEIRD

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Protein

D-alanine--D-alanine ligase

Gene
ddl, Mrub_0337, K649_01305
Organism
Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber)
Status
Unreviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.UniRule annotationSAAS annotations

Catalytic activityi

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

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.UniRule annotationSAAS annotations

Pathwayi

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi146 – 19954ATP By similarityUniRule 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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

LigaseUniRule annotationSAAS annotationsImported

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradationUniRule annotationSAAS annotations, Peptidoglycan synthesisUniRule annotationSAAS annotations

Keywords - Ligandi

ATP-bindingUniRule annotationSAAS annotations, MagnesiumUniRule annotationSAAS annotations, ManganeseUniRule annotationSAAS annotations, Metal-bindingUniRule annotationSAAS annotations, Nucleotide-binding

Enzyme and pathway databases

BioCyciMRUB504728:GI6U-342-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 ligase
D-alanylalanine synthetase
Gene namesi
Name:ddlUniRule annotationImported
Ordered Locus Names:Mrub_0337Imported
ORF Names:K649_01305Imported
OrganismiMeiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber)Imported
Taxonomic identifieri504728 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeMeiothermus
ProteomesiUP000006655: Chromosome, UP000013026: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotationSAAS annotations

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotations

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 317198ATP-grasp By similarityUniRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.UniRule annotation
Contains ATP-grasp domain.SAAS annotations

Phylogenomic databases

HOGENOMiHOG000011593.
KOiK01921.
OMAiQIDVIFP.

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]
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

MKVLLLAGGP PGEHEVSLSS ARGVLAAMPH PTELVVIAKD GRWLLGEDAY    50
EALRAGVAEQ GTHPFPPPVP WQHYDVVFPL LHGPLGEDGV IQGFLQLLRR 100
PYVGAGVASS ALCMDKDLCK RVLRQAGIPV VPWVTLYKGE PTPQPPFPPP 150
YFVKPANTGS SVGISKVKAD QDATRALAEA FAWDDKVLVE QGIEGVRELE 200
VALLGNIHAE ASVVGEITYQ SEFYDYETKY TEGKAQLHLP APIPPELSDE 250
IRATALEAYR ILGVRGMARV DFFLSPQGEL YLNEFNTIPG FTPTSMYPKL 300
WQATGLAYPD LLDRLVRLAL ER 322
Length:322
Mass (Da):35,231
Last modified:April 20, 2010 - v1
Checksum:i396C70BD2892732B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001743 Genomic DNA. Translation: ADD27115.1.
CP005385 Genomic DNA. Translation: AGK03569.1.
RefSeqiWP_013012634.1. NC_021081.1.
YP_003506135.1. NC_013946.1.
YP_007879066.1. NC_021081.1.

Genome annotation databases

EnsemblBacteriaiADD27115; ADD27115; Mrub_0337.
AGK03569; AGK03569; K649_01305.
GeneIDi15334879.
8878408.
KEGGimrb:Mrub_0337.
mre:K649_01305.
PATRICi35356778. VBIMeiRub128672_0343.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001743 Genomic DNA. Translation: ADD27115.1 .
CP005385 Genomic DNA. Translation: AGK03569.1 .
RefSeqi WP_013012634.1. NC_021081.1.
YP_003506135.1. NC_013946.1.
YP_007879066.1. NC_021081.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ADD27115 ; ADD27115 ; Mrub_0337 .
AGK03569 ; AGK03569 ; K649_01305 .
GeneIDi 15334879.
8878408.
KEGGi mrb:Mrub_0337.
mre:K649_01305.
PATRICi 35356778. VBIMeiRub128672_0343.

Phylogenomic databases

HOGENOMi HOG000011593.
KOi K01921.
OMAi QIDVIFP.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci MRUB504728:GI6U-342-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. 1 hit.
[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.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 35948 / DSM 1279 / VKM B-1258 / 21.
  2. "Non-Hybrid, Finished Microbial Genome Assemblies from Long-Read SMRT Sequencing Data."
    Klammer A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E., Turner S.W.
    Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: DSM 1279Imported.
  3. 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: September 3, 2014
This is version 37 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome

External Data

Dasty 3

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