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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Halobacteriovorax marinus (strain ATCC BAA-682 / DSM 15412 / SJ) (Bacteriovorax marinus)
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

Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

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.

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
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 bindingi280 – 2801Magnesium or manganese 1UniRule annotation
Metal bindingi293 – 2931Magnesium or manganese 1UniRule annotation
Metal bindingi293 – 2931Magnesium or manganese 2UniRule annotation
Metal bindingi295 – 2951Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi151 – 20656ATPUniRule 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

BioCyciBMAR862908:GJBX-1765-MONOMER.
UniPathwayiUPA00219.
UPA00219.

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 annotationImported
Ordered Locus Names:BMS_1867Imported
OrganismiHalobacteriovorax marinus (strain ATCC BAA-682 / DSM 15412 / SJ) (Bacteriovorax marinus)Imported
Taxonomic identifieri862908 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaBdellovibrionalesHalobacteriovoraceaeHalobacteriovorax
ProteomesiUP000008963 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Protein-protein interaction databases

STRINGi862908.BMS_1867.

Structurei

3D structure databases

ProteinModelPortaliE1X227.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini121 – 326206ATP-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.
OMAiYRIAFIG.

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]
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.

E1X227-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKNILLLCGG GGSEHEVSLR SANYIYDELE KVNLYNVFKV EIKANGDRVD
60 70 80 90 100
HHGQLCELRK AGELYYPSSD QTHKLDFAIP CIHGPPGENG VIQSIFELMG
110 120 130 140 150
LPYLGCSPEP SQTCFNKVST KLWLDALKVP NTPYIYLSDE SRESISAAEE
160 170 180 190 200
FFNANKDVYI KAASQGSSVG CYHVTSLEDL ESTILSAFKF SEYVLIERTL
210 220 230 240 250
KARELEVSAF EYNNEVVITA PGEIICPDGF YDYDQKYSND SATKTEVNAK
260 270 280 290 300
GLSAEQINDI KSYSLKAFKG LKLRHLSRID FFLTEEGKVY LNEINTFPGM
310 320
TSISMFPKMM ENHGVKFSEY LRKIIEEST
Length:329
Mass (Da):37,030
Last modified:November 30, 2010 - v1
Checksum:i93F4D612E4161D96
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FQ312005 Genomic DNA. Translation: CBW26687.1.
RefSeqiWP_014244468.1. NC_016620.1.
YP_005035652.1. NC_016620.1.

Genome annotation databases

EnsemblBacteriaiCBW26687; CBW26687; BMS_1867.
KEGGibmx:BMS_1867.
PATRICi42739739. VBIBacMar168520_1772.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FQ312005 Genomic DNA. Translation: CBW26687.1.
RefSeqiWP_014244468.1. NC_016620.1.
YP_005035652.1. NC_016620.1.

3D structure databases

ProteinModelPortaliE1X227.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi862908.BMS_1867.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCBW26687; CBW26687; BMS_1867.
KEGGibmx:BMS_1867.
PATRICi42739739. VBIBacMar168520_1772.

Phylogenomic databases

KOiK01921.
OMAiYRIAFIG.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciBMAR862908:GJBX-1765-MONOMER.

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]
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. "A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus."
    Crossman L.C., Chen H., Cerdeno-Tarraga A.M., Brooks K., Quail M.A., Pineiro S.A., Hobley L., Sockett R.E., Bentley S.D., Parkhill J., Williams H.N., Stine O.C.
    ISME J. 7:148-160(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-682 / DSM 15412 / SJImported.

Entry informationi

Entry nameiE1X227_HALMS
AccessioniPrimary (citable) accession number: E1X227
Entry historyi
Integrated into UniProtKB/TrEMBL: November 30, 2010
Last sequence update: November 30, 2010
Last modified: June 24, 2015
This is version 36 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

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.