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B2RIT4

- DDL_PORG3

UniProt

B2RIT4 - DDL_PORG3

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Protein

D-alanine--D-alanine ligase

Gene
ddl, PGN_0760
Organism
Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
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 bindingi277 – 2771Magnesium or manganese 1 By similarity
Metal bindingi290 – 2901Magnesium or manganese 1 By similarity
Metal bindingi290 – 2901Magnesium or manganese 2 By similarity
Metal bindingi292 – 2921Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi151 – 20656ATP By similarityAdd
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

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

BioCyciPGIN431947:GC9J-784-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:PGN_0760
OrganismiPorphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
Taxonomic identifieri431947 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaePorphyromonas
ProteomesiUP000008842: 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 – 330330D-alanine--D-alanine ligaseUniRule annotationPRO_1000091202Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi431947.PGN_0760.

Structurei

3D structure databases

ProteinModelPortaliB2RIT4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini122 – 323202ATP-graspAdd
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

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. 1 hit.
[Graphical view]
SUPFAMiSSF52440. SSF52440. 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.

B2RIT4-1 [UniParc]FASTAAdd to Basket

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MKKPIVAVIA GGYSGEHSVS LKSAAGILSW LGSEPFSAFL VLIERDRWSV    50
RVSEQREVPL DKNDFSFDLD DERIRFDYAY ITIHGTPGEN GLLQGYLDMI 100
GIPYNTGDTL VESLTFNKYV CNRFLSGFGI RIADSMRLTG RDTQPDVADL 150
TARMGLPLFV KPNVGGSSIA TTKVVEAAQL LPAIGQAFSE GEEVMIERLI 200
CGTEVTCGAF LRKKEVVALP VTEVVAHNEF FDFDAKYNGA VEEITPARIS 250
DEATRLIQTM TARIYELLNA RGIIRVDYII EADGIPTLLE VNTTPGMTPT 300
SFIPQQVRAA EMDMKEVLCT IIRDGLNETQ 330
Length:330
Mass (Da):36,369
Last modified:July 1, 2008 - v1
Checksum:i36097B6499FDB9EE
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP009380 Genomic DNA. Translation: BAG33279.1.
RefSeqiYP_001928876.1. NC_010729.1.

Genome annotation databases

EnsemblBacteriaiBAG33279; BAG33279; PGN_0760.
GeneIDi6329405.
KEGGipgn:PGN_0760.
PATRICi22974460. VBIPorGin26334_0750.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AP009380 Genomic DNA. Translation: BAG33279.1 .
RefSeqi YP_001928876.1. NC_010729.1.

3D structure databases

ProteinModelPortali B2RIT4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 431947.PGN_0760.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAG33279 ; BAG33279 ; PGN_0760 .
GeneIDi 6329405.
KEGGi pgn:PGN_0760.
PATRICi 22974460. VBIPorGin26334_0750.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci PGIN431947:GC9J-784-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.
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. "Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis."
    Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K.
    DNA Res. 15:215-225(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33277 / DSM 20709 / JCM 12257.

Entry informationi

Entry nameiDDL_PORG3
AccessioniPrimary (citable) accession number: B2RIT4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: July 1, 2008
Last modified: May 14, 2014
This is version 45 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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