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B6JB38

- DDL_OLICO

UniProt

B6JB38 - DDL_OLICO

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
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

Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi252 – 2521Magnesium or manganese 1UniRule annotation
Metal bindingi269 – 2691Magnesium or manganese 1UniRule annotation
Metal bindingi269 – 2691Magnesium or manganese 2UniRule annotation
Metal bindingi271 – 2711Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi130 – 18455ATPUniRule 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

BioCyciOCAR504832:GJPZ-2722-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:OCAR_5247, OCA5_c27220
OrganismiOligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
Taxonomic identifieri504832 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeOligotropha
ProteomesiUP000001678: Chromosome, UP000007730: 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 – 308308D-alanine--D-alanine ligasePRO_1000091199Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi504832.OCAR_5247.

Structurei

3D structure databases

ProteinModelPortaliB6JB38.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini103 – 302200ATP-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.
OMAiCLLEANT.
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. 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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B6JB38-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTALQHVAVL MGGWSSEREV SLRSGAACAA ALERKGYRVT RIDVQRDIAT
60 70 80 90 100
VLQNLKPDVA LVMLHGKPGE DGTIQGVLET LGIPYSHSGV LSSSLAMRKD
110 120 130 140 150
LAKTVMATAG VPVAEGLTLT RAEIAKAHVM APPYVIKPVA DGSSVGVFIV
160 170 180 190 200
TEDQAHPPQE LFRDDWPHGE ELLVEKYIAG RELTCAVIKG EASDVIEIVP
210 220 230 240 250
LLKFYDYEAK YSKGASKHVL PAPVLPFVYQ EVRRLTLAAH GALGCRGVSR
260 270 280 290 300
ADFRYDDRIE GTGGLVCLEV NTQPGMTETS LVPELAGYAG VAFDELVQWM

VEDASLDR
Length:308
Mass (Da):33,238
Last modified:December 16, 2008 - v1
Checksum:iFD911E66442DB8CA
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001196 Genomic DNA. Translation: ACI92379.1.
CP002826 Genomic DNA. Translation: AEI07416.1.
RefSeqiYP_002288244.1. NC_011386.1.
YP_004633657.1. NC_015684.1.

Genome annotation databases

EnsemblBacteriaiACI92379; ACI92379; OCAR_5247.
AEI07416; AEI07416; OCA5_c27220.
GeneIDi10847854.
6991234.
KEGGioca:OCAR_5247.
ocg:OCA5_c27220.
PATRICi22804427. VBIOliCar134280_1184.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001196 Genomic DNA. Translation: ACI92379.1 .
CP002826 Genomic DNA. Translation: AEI07416.1 .
RefSeqi YP_002288244.1. NC_011386.1.
YP_004633657.1. NC_015684.1.

3D structure databases

ProteinModelPortali B6JB38.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 504832.OCAR_5247.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACI92379 ; ACI92379 ; OCAR_5247 .
AEI07416 ; AEI07416 ; OCA5_c27220 .
GeneIDi 10847854.
6991234.
KEGGi oca:OCAR_5247.
ocg:OCA5_c27220.
PATRICi 22804427. VBIOliCar134280_1184.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci OCAR504832:GJPZ-2722-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.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T."
    Paul D., Bridges S., Burgess S.C., Dandass Y., Lawrence M.L.
    J. Bacteriol. 190:5531-5532(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49405 / DSM 1227 / OM5.
  2. "Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5."
    Volland S., Rachinger M., Strittmatter A., Daniel R., Gottschalk G., Meyer O.
    J. Bacteriol. 193:5043-5043(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49405 / DSM 1227 / OM5.

Entry informationi

Entry nameiDDL_OLICO
AccessioniPrimary (citable) accession number: B6JB38
Secondary accession number(s): F8BV61
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: December 16, 2008
Last modified: October 29, 2014
This is version 46 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