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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Thermodesulfobacterium geofontis (strain OPF15)
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.

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 bindingi259 – 2591Magnesium or manganese 1UniRule annotation
Metal bindingi271 – 2711Magnesium or manganese 1UniRule annotation
Metal bindingi271 – 2711Magnesium or manganese 2UniRule annotation
Metal bindingi273 – 2731Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi135 – 19056ATPUniRule 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

BioCyciTSP795359:GI1V-1061-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 annotation
Ordered Locus Names:TOPB45_1022Imported
OrganismiThermodesulfobacterium geofontis (strain OPF15)Imported
Taxonomic identifieri795359 [NCBI]
Taxonomic lineageiBacteriaThermodesulfobacteriaThermodesulfobacterialesThermodesulfobacteriaceaeThermodesulfobacterium
ProteomesiUP000006583 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

STRINGi795359.TOPB45_1022.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini106 – 304199ATP-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.
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.

F8C5X5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSIGVLKIA LLAGGTSSER EVSLKGAEVV KKALEKLGHK YEFFDPAQDL
60 70 80 90 100
PKLAQRAKEF DCAFLVVHGP GGEDGTLQGF LDSIGLPYQG AGVLGSALAM
110 120 130 140 150
HKGISKSLYK LAGLNVPEGK TFSKDSSFEI IKTYGEKIGF PLVVKPATQG
160 170 180 190 200
SSIGLSVVKD KKDLKKAVEA AFNVDREIIL EKYLKGKEIT VGILDDKPLP
210 220 230 240 250
VVEIVPKVSE IFDYETKYTP GLSEEICPAR LSERLTKKAQ EYGLIAHKTL
260 270 280 290 300
KLRHYSRTDM IIVEDEIYVL ETNTIPGMTE TSLLPLAAKV AGYSFPALIQ
310
KLLELTLRDK NT
Length:312
Mass (Da):34,043
Last modified:September 21, 2011 - v1
Checksum:iA2C5CA02F7067ACC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002829 Genomic DNA. Translation: AEH23116.1.
RefSeqiWP_013909814.1. NC_015682.1.
YP_004628044.1. NC_015682.1.

Genome annotation databases

EnsemblBacteriaiAEH23116; AEH23116; TOPB45_1022.
KEGGitop:TOPB45_1022.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002829 Genomic DNA. Translation: AEH23116.1.
RefSeqiWP_013909814.1. NC_015682.1.
YP_004628044.1. NC_015682.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi795359.TOPB45_1022.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEH23116; AEH23116; TOPB45_1022.
KEGGitop:TOPB45_1022.

Phylogenomic databases

KOiK01921.
OMAiPFLLEMN.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciTSP795359:GI1V-1061-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. 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 sequence of Thermodesulfobacterium sp. OPB45."
    Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Mikhailova N., Davenport K., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Pagani I., Hamilton-Brehm S., Elkins J., Woyke T.
    Submitted (JUN-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: OPB45Imported.

Entry informationi

Entry nameiF8C5X5_THEGP
AccessioniPrimary (citable) accession number: F8C5X5
Entry historyi
Integrated into UniProtKB/TrEMBL: September 21, 2011
Last sequence update: September 21, 2011
Last modified: June 24, 2015
This is version 30 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.