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Q2RVU7

- DDL_RHORT

UniProt

Q2RVU7 - DDL_RHORT

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Rhodospirillum rubrum (strain ATCC 11170 / NCIB 8255)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi251 – 2511Magnesium or manganese 1UniRule annotation
Metal bindingi263 – 2631Magnesium or manganese 1UniRule annotation
Metal bindingi263 – 2631Magnesium or manganese 2UniRule annotation
Metal bindingi265 – 2651Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi130 – 18354ATPUniRule 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. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. 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

BioCyciRRUB269796:GCN1-968-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 ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:Rru_A0947
OrganismiRhodospirillum rubrum (strain ATCC 11170 / NCIB 8255)
Taxonomic identifieri269796 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodospirillalesRhodospirillaceaeRhodospirillum
ProteomesiUP000001929: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 302302D-alanine--D-alanine ligasePRO_0000341168Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi269796.Rru_A0947.

Structurei

3D structure databases

ProteinModelPortaliQ2RVU7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini104 – 296193ATP-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.
OMAiCSGYSRV.
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.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q2RVU7-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKRVTVLMG GFSTERAVSL NSGAAAGEAL RQAGYAVTLL DVGRDVAAFI
60 70 80 90 100
AALTQTRPDV VFNALHGRFG EDGAIQGILD IMALPYTHSG RLASAIAMDK
110 120 130 140 150
PSAKLVFERF AIPVAPHVVA DRASVLAETA MARPYVVKPL DQGSSVGVTI
160 170 180 190 200
VTSETNDLPF SRDDWPYGRQ VMVERFIPGR ELTVGVMGDK ALGVTEIVTD
210 220 230 240 250
HRFYDYDAKY AQGGSRHIVP APVAPEVFAQ AQELSVLAHQ ALGCRGVSRA
260 270 280 290 300
DLRFDGETLY MLEVNTQPGM TDTSLVPEQA LHAGISFPDL VTWLVETAQC

DA
Length:302
Mass (Da):32,390
Last modified:January 24, 2006 - v1
Checksum:iCA4B2D25810181F1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000230 Genomic DNA. Translation: ABC21748.1.
RefSeqiWP_011388702.1. NC_007643.1.
YP_426035.1. NC_007643.1.

Genome annotation databases

EnsemblBacteriaiABC21748; ABC21748; Rru_A0947.
GeneIDi3834404.
KEGGirru:Rru_A0947.
PATRICi23325488. VBIRhoRub82919_1003.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000230 Genomic DNA. Translation: ABC21748.1 .
RefSeqi WP_011388702.1. NC_007643.1.
YP_426035.1. NC_007643.1.

3D structure databases

ProteinModelPortali Q2RVU7.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 269796.Rru_A0947.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABC21748 ; ABC21748 ; Rru_A0947 .
GeneIDi 3834404.
KEGGi rru:Rru_A0947.
PATRICi 23325488. VBIRhoRub82919_1003.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci RRUB269796:GCN1-968-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.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete sequence of the chromosome of Rhodospirillum rubrum ATCC 11170."
    Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T., Hammon N., Israni S., Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M.
    , Kyrpides N., Mavrommatis K., Richardson P., Zhang Y., Roberts G., Reslewic S., Zhou S., Schwartz D.C.
    Submitted (DEC-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S.1.

Entry informationi

Entry nameiDDL_RHORT
AccessioniPrimary (citable) accession number: Q2RVU7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: January 24, 2006
Last modified: November 26, 2014
This is version 73 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, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3