Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

D-alanine--D-alanine ligase

Gene

ddlA

Organism
Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)
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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi242 – 2421Magnesium or manganese 1UniRule annotation
Metal bindingi255 – 2551Magnesium or manganese 1UniRule annotation
Metal bindingi255 – 2551Magnesium or manganese 2UniRule annotation
Metal bindingi257 – 2571Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi125 – 17652ATPUniRule 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

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:ddlAImported
Synonyms:ddlUniRule annotation
Ordered Locus Names:HTH_1800Imported, Hydth_1782Imported
OrganismiHydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)Imported
Taxonomic identifieri608538 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeHydrogenobacter
ProteomesiUP000002574 Componenti: Chromosome UP000008982 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Structurei

3D structure databases

ProteinModelPortaliD3DK92.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini99 – 288190ATP-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

HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.

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. 2 hits.
[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.

D3DK92-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRVVVLMGGR SEEREISLKT GEAVLRAIRE LGHEAIPLDL EENLCQKLLE
60 70 80 90 100
IKPDKVFIAL HGTYGEDGRV QGLLDILGIP YTGSGVLGSC LAMDKDITKK
110 120 130 140 150
ILTFHRIPVP AGICVRRGET FEWHSFPAVV KPADQGSSVG LFLVKDHDEL
160 170 180 190 200
ENAVREVLSI SHKVLIEEYI IGRDITVGIL KGEALPPVEI KPKKGIYDYE
210 220 230 240 250
SKYTKGMSDY VFLEDEKLIK KLQDIALMVH KYLELKDISR VDFRLSEDGV
260 270 280
AYVLEANTIP GMTELSLFPM MCKKKGIEFK EMIHMLLS
Length:288
Mass (Da):32,326
Last modified:March 23, 2010 - v1
Checksum:i438D54741C8BC778
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002221 Genomic DNA. Translation: ADO46163.1.
AP011112 Genomic DNA. Translation: BAI70244.1.
RefSeqiWP_012964424.1. NC_017161.1.
YP_003433445.1. NC_013799.1.
YP_005512456.1. NC_017161.1.

Genome annotation databases

EnsemblBacteriaiADO46163; ADO46163; Hydth_1782.
BAI70244; BAI70244; HTH_1800.
KEGGihte:Hydth_1782.
hth:HTH_1800.
PATRICi32212547. VBIHydThe36152_1805.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002221 Genomic DNA. Translation: ADO46163.1.
AP011112 Genomic DNA. Translation: BAI70244.1.
RefSeqiWP_012964424.1. NC_017161.1.
YP_003433445.1. NC_013799.1.
YP_005512456.1. NC_017161.1.

3D structure databases

ProteinModelPortaliD3DK92.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADO46163; ADO46163; Hydth_1782.
BAI70244; BAI70244; HTH_1800.
KEGGihte:Hydth_1782.
hth:HTH_1800.
PATRICi32212547. VBIHydThe36152_1805.

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.

Enzyme and pathway databases

UniPathwayiUPA00219.

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. 2 hits.
[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 genome sequence of the thermophilic, obligately chemolithoautotrophic hydrogen-oxidizing bacterium Hydrogenobacter thermophilus TK-6."
    Arai H., Kanbe H., Ishii M., Igarashi Y.
    J. Bacteriol. 192:2651-2652(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 6534 / IAM 12695 / TK-6 [Tokyo]Imported and TK-6.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 6534 / IAM 12695 / TK-6 [JGI]Imported and TK-6Imported.

Entry informationi

Entry nameiD3DK92_HYDTT
AccessioniPrimary (citable) accession number: D3DK92
Entry historyi
Integrated into UniProtKB/TrEMBL: March 23, 2010
Last sequence update: March 23, 2010
Last modified: April 29, 2015
This is version 45 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.