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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nitratifractor salsuginis (strain DSM 16511 / JCM 12458 / E9I37-1)
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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi287 – 2871Magnesium or manganese 1UniRule annotation
Metal bindingi299 – 2991Magnesium or manganese 1UniRule annotation
Metal bindingi299 – 2991Magnesium or manganese 2UniRule annotation
Metal bindingi301 – 3011Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi162 – 21554ATPUniRule 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

BioCyciNSAL749222:GHWN-1981-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:Nitsa_1940Imported
OrganismiNitratifractor salsuginis (strain DSM 16511 / JCM 12458 / E9I37-1)Imported
Taxonomic identifieri749222 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesNitratifractor
ProteomesiUP000008633 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini136 – 335200ATP-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

HOGENOMiHOG000102494.
KOiK01921.

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]
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.

E6X2H8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIAILFGGS SYEHEISIVS AITLKKSLKR NEPLFIFVDS AREFYLIEPE
60 70 80 90 100
KMKSKTFSSG EYKKAKKLSL ERGGFSMAGG LLGGRKPLEF DCLLNLIHGR
110 120 130 140 150
DGEDGKIAGM MEFFRIPFIG PRLEASVMSY SKLNTKLLAQ ALGISVLEYE
160 170 180 190 200
LLRKEGPRKL SRLEYPVIVK PVHLGSSIGV SIVREASQLD YALDVAFEFD
210 220 230 240 250
DLVIVEPFVE GIREYNLAGC KTSAWELSLI EEPQKEEFLD FDKKYMDFSR
260 270 280 290 300
DTRVQEAVID APLRERLETA FKNIYDPLFL GSLIRCDFFV VEEKVYLNEI
310 320 330 340
NPIPGSMAHY LFDDFEGIIE RLAKNLPKEK SIPVDYRYIH SIQSAKGKA
Length:349
Mass (Da):39,639
Last modified:March 7, 2011 - v1
Checksum:i302336630C8898DF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002452 Genomic DNA. Translation: ADV47183.1.
RefSeqiWP_013554868.1. NC_014935.1.
YP_004168932.1. NC_014935.1.

Genome annotation databases

EnsemblBacteriaiADV47183; ADV47183; Nitsa_1940.
GeneIDi10148740.
KEGGinsa:Nitsa_1940.
PATRICi46985417. VBINitSal150288_1918.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002452 Genomic DNA. Translation: ADV47183.1.
RefSeqiWP_013554868.1. NC_014935.1.
YP_004168932.1. NC_014935.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADV47183; ADV47183; Nitsa_1940.
GeneIDi10148740.
KEGGinsa:Nitsa_1940.
PATRICi46985417. VBINitSal150288_1918.

Phylogenomic databases

HOGENOMiHOG000102494.
KOiK01921.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciNSAL749222:GHWN-1981-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]
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 16511 / JCM 12458 / E9I37-1Imported.

Entry informationi

Entry nameiE6X2H8_NITSE
AccessioniPrimary (citable) accession number: E6X2H8
Entry historyi
Integrated into UniProtKB/TrEMBL: March 7, 2011
Last sequence update: March 7, 2011
Last modified: March 3, 2015
This is version 29 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.