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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Verrucosispora maris (strain AB-18-032)
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 bindingi324 – 3241Magnesium or manganese 1UniRule annotation
Metal bindingi338 – 3381Magnesium or manganese 1UniRule annotation
Metal bindingi338 – 3381Magnesium or manganese 2UniRule annotation
Metal bindingi340 – 3401Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi198 – 25356ATPUniRule 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

BioCyciVMAR263358:GI1P-1024-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:VAB18032_09595Imported
OrganismiVerrucosispora maris (strain AB-18-032)Imported
Taxonomic identifieri263358 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesMicromonosporineaeMicromonosporaceaeVerrucosispora
ProteomesiUP000008308 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
Domaini167 – 371205ATP-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.

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.

F4F5K5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSERHSGGAR RDGGGRPQVI GVLFGGPSAE HEVSCASALG VARALVGGGY
60 70 80 90 100
QVVALGVTRQ GRLRLVPEET LAAHIDGTAA ARAIDDRLSV TGSAVELRAG
110 120 130 140 150
ERPGTALVTG AESPGEVHAV LDVVFPVLHG PYGEDGVVQG LLESLGVPYV
160 170 180 190 200
GCGILASAVG MDKVAMKRAL RAEGVPITPH VWFDEHTYRT TEDVEKLVVG
210 220 230 240 250
LRRPLFVKPA RMGSSIGISR VTEDDDLAAA VEEALRHDNL VVVEQGVTGR
260 270 280 290 300
ELECGVLGGT RPEASTVGEV RVTGGWFDYQ QKYFGDADPM VVPAVLPDEV
310 320 330 340 350
TERIRDLSLR AFAAIGGWGL ARVDFLYDES AGELYVNELN TMPGFTAHSM
360 370 380
YPKVWAAAGV GYQQIVDRLV ALAVERRASR PTSQEGQA
Length:388
Mass (Da):41,114
Last modified:June 27, 2011 - v1
Checksum:i868B27B093286B07
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002638 Genomic DNA. Translation: AEB43037.1.
RefSeqiYP_004403637.1. NC_015434.1.

Genome annotation databases

EnsemblBacteriaiAEB43037; AEB43037; VAB18032_09595.
GeneIDi10449789.
KEGGivma:VAB18032_09595.
PATRICi54470320. VBIVerMar92278_1066.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002638 Genomic DNA. Translation: AEB43037.1.
RefSeqiYP_004403637.1. NC_015434.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEB43037; AEB43037; VAB18032_09595.
GeneIDi10449789.
KEGGivma:VAB18032_09595.
PATRICi54470320. VBIVerMar92278_1066.

Phylogenomic databases

KOiK01921.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciVMAR263358:GI1P-1024-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. "Genome sequence of the abyssomicin- and proximicin-producing marine actinomycete Verrucosispora maris AB-18-032."
    Roh H., Uguru G.C., Ko H.J., Kim S., Kim B.Y., Goodfellow M., Bull A.T., Kim K.H., Bibb M.J., Choi I.G., Stach J.E.
    J. Bacteriol. 193:3391-3392(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AB-18-032Imported.

Entry informationi

Entry nameiF4F5K5_VERMA
AccessioniPrimary (citable) accession number: F4F5K5
Entry historyi
Integrated into UniProtKB/TrEMBL: June 27, 2011
Last sequence update: June 27, 2011
Last modified: March 31, 2015
This is version 26 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.