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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Bacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42)
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

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation
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 bindingi292 – 2921Magnesium or manganese 1UniRule annotation
Metal bindingi305 – 3051Magnesium or manganese 1UniRule annotation
Metal bindingi305 – 3051Magnesium or manganese 2UniRule annotation
Metal bindingi307 – 3071Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi166 – 22156ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

BioCyciBAMY326423:GCM4-488-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:RBAM_004900
OrganismiBacillus amyloliquefaciens subsp. plantarum (strain DSM 23117 / BGSC 10A6 / FZB42)
Taxonomic identifieri326423 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001120 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 354354D-alanine--D-alanine ligasePRO_0000341058Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi326423.RBAM_004900.

Structurei

3D structure databases

ProteinModelPortaliA7Z1L3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini133 – 338206ATP-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.
OMAiWFPILHG.
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]
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.

A7Z1L3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYGGKSAEHN VSLQTALAVT KALNTEKFDI HPIYITEKGE WQRGPLLTEP
60 70 80 90 100
VSNVKMLQLE QNGESFALSA LNREMFPEAS PDEKAPIDVV FPLLHGPNGE
110 120 130 140 150
DGTIQGLLEL LNVPYVGNGV LASSAGMDKV IMKHLFAQAG LPQAKYAAFL
160 170 180 190 200
KKDWKQTPDS CLQQVEKELG YPCFVKPANL GSSVGISKCR NREELEKAFE
210 220 230 240 250
LAFEYDRKIV VEEGIAGREI EIGVLGNDEP KCSAVGEIAP KTDFYDYKAK
260 270 280 290 300
YEDGDTDLMI PAQVTDEQYA EISEMAIKAF KAIDGSGLVR ADFFLTNDGQ
310 320 330 340 350
VLINEVNTMP GFTPFSMFPL LWKEAGVDYS DLIEQLVELA KERHAEKQLI

KHTF
Length:354
Mass (Da):39,216
Last modified:October 23, 2007 - v1
Checksum:iE55EAFAD7042E84C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000560 Genomic DNA. Translation: ABS72889.1.
RefSeqiWP_012116864.1. NC_009725.1.
YP_001420120.1. NC_009725.1.

Genome annotation databases

EnsemblBacteriaiABS72889; ABS72889; RBAM_004900.
KEGGibay:RBAM_004900.
PATRICi18745902. VBIBacAmy31356_0463.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000560 Genomic DNA. Translation: ABS72889.1.
RefSeqiWP_012116864.1. NC_009725.1.
YP_001420120.1. NC_009725.1.

3D structure databases

ProteinModelPortaliA7Z1L3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi326423.RBAM_004900.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABS72889; ABS72889; RBAM_004900.
KEGGibay:RBAM_004900.
PATRICi18745902. VBIBacAmy31356_0463.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciBAMY326423:GCM4-488-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]
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 23117 / BGSC 10A6 / FZB42.

Entry informationi

Entry nameiDDL_BACA2
AccessioniPrimary (citable) accession number: A7Z1L3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: October 23, 2007
Last modified: May 27, 2015
This is version 60 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

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.