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F6IJ61

- F6IJ61_9SPHN

UniProt

F6IJ61 - F6IJ61_9SPHN

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Novosphingobium sp. PP1Y
Status
Unreviewed - 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

Note: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi276 – 2761Magnesium or manganese 1UniRule annotation
Metal bindingi292 – 2921Magnesium or manganese 1UniRule annotation
Metal bindingi292 – 2921Magnesium or manganese 2UniRule annotation
Metal bindingi294 – 2941Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi152 – 20857ATPUniRule 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

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

BioCyciNSP702113:GJD2-718-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
ORF Names:PP1Y_AT7490Imported
OrganismiNovosphingobium sp. PP1YImported
Taxonomic identifieri702113 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeNovosphingobium
ProteomesiUP000009242: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini125 – 325201ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation
Contains ATP-grasp domain.SAAS annotation

Phylogenomic databases

KOiK01921.

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.

F6IJ61-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGNPARRHAC RRAQHTASRY TVSLPKLHVA VLMGGWSHER SVSLMSGEGV
60 70 80 90 100
AKALESKGHK VTRIDMDRNV ALRLSEAAPD VVFNALHGAP GEDGTVQGMM
110 120 130 140 150
DLMGLTYTHS GLATSVIAID KELTKQALVP HGIPMPGGRI VASEDLYAGD
160 170 180 190 200
PLPRPYVLKP VNEGSSVGVA IVMDASNYGN PIRRDAAGPW QEFDHLLAEP
210 220 230 240 250
YIRGRELTTA VIGDRALLVT ELKPKSGFYD FDSKYTDGLT EHVCPAEIPD
260 270 280 290 300
EIAQACKDLA LRAHRLLGCK GTSRSDFRWD DTQGVEGLFL LETNTQPGMT
310 320 330 340
PLSLVPEQAR ACGMEYADLV EAIIAEALED ARSKQAAGAV KGAE
Length:344
Mass (Da):37,049
Last modified:July 27, 2011 - v1
Checksum:i10E1047439B4C474
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FR856862 Genomic DNA. Translation: CCA91687.1.
RefSeqiWP_013832104.1. NC_015580.1.
YP_004533505.1. NC_015580.1.

Genome annotation databases

EnsemblBacteriaiCCA91687; CCA91687; PP1Y_AT7490.
GeneIDi10717485.
KEGGinpp:PP1Y_AT7490.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FR856862 Genomic DNA. Translation: CCA91687.1 .
RefSeqi WP_013832104.1. NC_015580.1.
YP_004533505.1. NC_015580.1.

3D structure databases

ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CCA91687 ; CCA91687 ; PP1Y_AT7490 .
GeneIDi 10717485.
KEGGi npp:PP1Y_AT7490.

Phylogenomic databases

KOi K01921.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci NSP702113:GJD2-718-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. "De novo sequencing and assembly of the whole genome of Novosphingobium sp. strain PP1Y."
    D'Argenio V., Petrillo M., Cantiello P., Naso B., Cozzuto L., Notomista E., Paolella G., Di Donato A., Salvatore F.
    J. Bacteriol. 193:4296-4296(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiF6IJ61_9SPHN
AccessioniPrimary (citable) accession number: F6IJ61
Entry historyi
Integrated into UniProtKB/TrEMBL: July 27, 2011
Last sequence update: July 27, 2011
Last modified: November 26, 2014
This is version 23 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