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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Desulfitobacterium dehalogenans (strain ATCC 51507 / DSM 9161 / JW/IU-DC1)
Status
Unreviewed-Annotation score: 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

Protein has several cofactor binding sites:
  • Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation
  • Mg2+, Mn2+Note: Binds 2 magnesium or manganese ions per subunit.

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotationSAAS annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi299 – 2991Magnesium or manganese 1UniRule annotation
Metal bindingi312 – 3121Magnesium or manganese 1UniRule annotation
Metal bindingi312 – 3121Magnesium or manganese 2UniRule annotation
Metal bindingi314 – 3141Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi173 – 22856ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

BioCyciDDEH756499:GLCG-2177-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotationSAAS annotation (EC:6.3.2.4UniRule annotationSAAS annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:Desde_2184Imported
OrganismiDesulfitobacterium dehalogenans (strain ATCC 51507 / DSM 9161 / JW/IU-DC1)Imported
Taxonomic identifieri756499 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptococcaceaeDesulfitobacterium
ProteomesiUP000006053 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini140 – 345206ATP-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

KOiK01921.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
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.

I4A995-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRQKIIILF GGQSGEHEVS LNSASSVLKA IDKEKYEVET LGISKSGQWH
60 70 80 90 100
WGIRPEQWQQ DPTLQGILVN LVHDPSNPRF IALDGSTLPQ DGTFDLIFPV
110 120 130 140 150
LHGPFGEDGT IQGLFEMANI PYAGSGVLGS ALGMDKDRMK AVFTEAGLPQ
160 170 180 190 200
APYLTVLRTT LQKMMEKVLH DIEHSLGYPC FVKPANLGSS VGISKARNRE
210 220 230 240 250
ELINALHLAA EYDRKIVVEQ NIVGREIELS VLGNEDAKAS IPGEILPSKD
260 270 280 290 300
FYDYEAKYID TGSRLVIPAP LDQEVVKSLQ EKAVAAFKAV EACGLSRVDF
310 320 330 340 350
FVTEGNQIYI NEINTMPGFT QISMYPKLWE ASGIPYSELI TQLIELGFQR
360
FRDSRSRKIS L
Length:361
Mass (Da):40,016
Last modified:September 5, 2012 - v1
Checksum:i8C34B465AF5F71C7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP003348 Genomic DNA. Translation: AFM00530.1.
RefSeqiWP_014794016.1. NC_018017.1.
YP_006430323.1. NC_018017.1.

Genome annotation databases

EnsemblBacteriaiAFM00530; AFM00530; Desde_2184.
KEGGiddh:Desde_2184.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP003348 Genomic DNA. Translation: AFM00530.1.
RefSeqiWP_014794016.1. NC_018017.1.
YP_006430323.1. NC_018017.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAFM00530; AFM00530; Desde_2184.
KEGGiddh:Desde_2184.

Phylogenomic databases

KOiK01921.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciDDEH756499:GLCG-2177-MONOMER.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
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]
ProtoNetiSearch...

Publicationsi

  1. "Complete sequence of Desulfitobacterium dehalogenans ATCC 51507."
    Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Ovchinnikova G., Teshima H., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Kruse T.
    , de Vos W.M., Smidt H., Woyke T.
    Submitted (JUN-2012) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51507 / DSM 9161 / JW/IU-DC1Imported.

Entry informationi

Entry nameiI4A995_DESDJ
AccessioniPrimary (citable) accession number: I4A995
Entry historyi
Integrated into UniProtKB/TrEMBL: September 5, 2012
Last sequence update: September 5, 2012
Last modified: June 24, 2015
This is version 22 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.