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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Thermosipho melanesiensis (strain BI429 / DSM 12029)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.UniRule annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 2 magnesium or manganese ions per subunit.By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi296 – 2961Magnesium or manganese 1UniRule annotation
Metal bindingi307 – 3071Magnesium or manganese 1UniRule annotation
Metal bindingi307 – 3071Magnesium or manganese 2UniRule annotation
Metal bindingi309 – 3091Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi167 – 22256ATPUniRule 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

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

BioCyciTMEL391009:GHM1-510-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligaseUniRule annotation (EC:6.3.2.4UniRule annotation)
Alternative name(s):
D-Ala-D-Ala ligaseUniRule annotation
D-alanylalanine synthetaseUniRule annotation
Gene namesi
Name:ddlUniRule annotation
Ordered Locus Names:Tmel_0486
OrganismiThermosipho melanesiensis (strain BI429 / DSM 12029)
Taxonomic identifieri391009 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermosipho
ProteomesiUP000001110: Chromosome

Subcellular locationi

Cytoplasm 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 – 361361D-alanine--D-alanine ligasePRO_1000030516Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi391009.Tmel_0486.

Structurei

3D structure databases

ProteinModelPortaliA6LKA2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini139 – 336198ATP-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

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiYRIAFIG.
OrthoDBiEOG64BQ73.

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]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A6LKA2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLNIGIFFGS KSVEHEISII TAQQVLSSID RKKYNVIPIY ISKSGEWFTG
60 70 80 90 100
KVLEDLETFK DFDKLEKKAK KIDSFSVKNN KLLLKYGLKK QTIDFCFLVF
110 120 130 140 150
HGTNGEDGTF QGMCEIFGIP YSGCNHFSSA FTMDKVVTKL LLKEKEISVV
160 170 180 190 200
DFEYTTEINE EFFKRCEKNL GYPMIVKPAR LGSSIGVSKV VDRKNFEEAV
210 220 230 240 250
KNVLLFDNKV LVEKWINARE INCAVMGYKN IFVSELEEIN KKNDFFNFEE
260 270 280 290 300
KYFKKGKKFS NHIIPARIDE NLKNKIKEIA KDTFKILECS GNVRIDFLIA
310 320 330 340 350
DKIYVNEINT IPGALSFYIW QKSGFTFSQI IDNMINMGLE RFKDKKIVSI
360
DTNILKIKVG K
Length:361
Mass (Da):41,621
Last modified:July 24, 2007 - v1
Checksum:iAA24E4FCADFC1E01
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000716 Genomic DNA. Translation: ABR30353.1.
RefSeqiWP_012056714.1. NC_009616.1.
YP_001305738.1. NC_009616.1.

Genome annotation databases

EnsemblBacteriaiABR30353; ABR30353; Tmel_0486.
GeneIDi5298236.
KEGGitme:Tmel_0486.
PATRICi23922131. VBITheMel19269_0511.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000716 Genomic DNA. Translation: ABR30353.1.
RefSeqiWP_012056714.1. NC_009616.1.
YP_001305738.1. NC_009616.1.

3D structure databases

ProteinModelPortaliA6LKA2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi391009.Tmel_0486.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABR30353; ABR30353; Tmel_0486.
GeneIDi5298236.
KEGGitme:Tmel_0486.
PATRICi23922131. VBITheMel19269_0511.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiYRIAFIG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciTMEL391009:GHM1-510-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]
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: BI429 / DSM 12029.

Entry informationi

Entry nameiDDL_THEM4
AccessioniPrimary (citable) accession number: A6LKA2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 24, 2007
Last modified: March 4, 2015
This is version 57 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, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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.