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Q1LIM8

- DDL_RALME

UniProt

Q1LIM8 - DDL_RALME

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Protein
D-alanine--D-alanine ligase
Gene
ddl, Rmet_3126
Organism
Ralstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

Functioni

Cell wall formation By similarity.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 bindingi266 – 2661Magnesium or manganese 1 By similarity
Metal bindingi279 – 2791Magnesium or manganese 1 By similarity
Metal bindingi279 – 2791Magnesium or manganese 2 By similarity
Metal bindingi281 – 2811Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi139 – 19456ATP By similarity
Add
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
Complete GO annotation...

GO - Biological processi

  1. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciCMET266264:GJ5G-3335-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:Rmet_3126
OrganismiRalstonia metallidurans (strain CH34 / ATCC 43123 / DSM 2839)
Taxonomic identifieri266264 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeCupriavidus
ProteomesiUP000002429: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 327327D-alanine--D-alanine ligaseUniRule annotation
PRO_0000341160Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi266264.Rmet_3126.

Structurei

3D structure databases

ProteinModelPortaliQ1LIM8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini113 – 312200ATP-grasp
Add
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiKLAFQYD.
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.

Q1LIM8-1 [UniParc]FASTAAdd to Basket

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MSFVAHPNID PKSLGKVGVL LGGKSAEREI SLLSGNGVLA ALKSRGVDAH    50
PFDPGLQPIS ELAAAGFDRV FIALHGRYGE DGTMQGLLEQ LGIPYTGSGV 100
LASALAMDKQ ATKRLWMTHG LATPRFAMLY ANTDFDAVVA DLGLPLIVKP 150
AREGSSIGLT KVIAADQMRA AFEKAAGLDA DVIAETFIDG AELTCPIVGE 200
GPTAEALPVI KIVAPESNYD YQNKYFTDDT QYLCPSTLPD ALEREVRALA 250
VEAFRVLGCR GWARADVMLT RDGKPYLLEM NTSPGMTGHS LVPMAARANG 300
ISYEDFVMQV LAAATLDLHP NEHWKPE 327
Length:327
Mass (Da):34,968
Last modified:May 30, 2006 - v1
Checksum:iE9968DC61E896386
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000352 Genomic DNA. Translation: ABF09998.1.
RefSeqiWP_011517618.1. NC_007973.1.
YP_585267.1. NC_007973.1.

Genome annotation databases

EnsemblBacteriaiABF09998; ABF09998; Rmet_3126.
GeneIDi4039955.
KEGGirme:Rmet_3126.
PATRICi20290887. VBIRalMet4734_3518.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000352 Genomic DNA. Translation: ABF09998.1 .
RefSeqi WP_011517618.1. NC_007973.1.
YP_585267.1. NC_007973.1.

3D structure databases

ProteinModelPortali Q1LIM8.
ModBasei Search...

Protein-protein interaction databases

STRINGi 266264.Rmet_3126.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABF09998 ; ABF09998 ; Rmet_3126 .
GeneIDi 4039955.
KEGGi rme:Rmet_3126.
PATRICi 20290887. VBIRalMet4734_3518.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci CMET266264:GJ5G-3335-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CH34 / ATCC 43123 / DSM 2839.

Entry informationi

Entry nameiDDL_RALME
AccessioniPrimary (citable) accession number: Q1LIM8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: May 30, 2006
Last modified: September 3, 2014
This is version 66 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

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