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Protein

D-alanine--D-alanine ligase B

Gene

ddlB

Organism
Salmonella typhi
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Cell wall formation.By similarity

Catalytic activityi

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

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.
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 bindingi257 – 2571Magnesium or manganese 1By similarity
Metal bindingi270 – 2701Magnesium or manganese 1By similarity
Metal bindingi270 – 2701Magnesium or manganese 2By similarity
Metal bindingi272 – 2721Magnesium or manganese 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18956ATPBy similarityAdd
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

UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase B (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase B
D-alanylalanine synthetase B
Gene namesi
Name:ddlB
Ordered Locus Names:STY0150, t0134
OrganismiSalmonella typhi
Taxonomic identifieri90370 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000000541 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 306305D-alanine--D-alanine ligase BPRO_0000177869Add
BLAST

Interactioni

Subunit structurei

Monomer.By similarity

Protein-protein interaction databases

STRINGi220341.STY0150.

Structurei

3D structure databases

ProteinModelPortaliQ8Z9G7.
SMRiQ8Z9G7. Positions 1-306.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 303203ATP-graspAdd
BLAST

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.Curated
Contains 1 ATP-grasp domain.Curated

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiKYTEGFA.
OrthoDBiEOG6ND0KB.

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q8Z9G7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADKIAVLLG GTSAERDVSL NSGAAVLAGL REGGIDAHPV DPQEVDVAQL
60 70 80 90 100
KAMGFQKVFI ALHGRGGEDG TLQGMLELLG LPYTGSGVMA SALSMDKLRS
110 120 130 140 150
KLLWQGAGLP VAPWVALTRA EFEKGLSEEQ KARISALGLP LIVKPSREGS
160 170 180 190 200
SVGMTKVVEE NALQGALSLA FQHDDEILIE KWLCGPEFTV AIVGEEILPS
210 220 230 240 250
IRIQPAGTFY DYEAKYLSDE TQYFCPAGLE ASQEAALQSL VLQAWKALGC
260 270 280 290 300
TGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR

ILELAD
Length:306
Mass (Da):32,650
Last modified:January 23, 2007 - v3
Checksum:i241275EB0D9D10B5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL513382 Genomic DNA. Translation: CAD01287.1.
AE014613 Genomic DNA. Translation: AAO67866.1.
RefSeqiNP_454742.1. NC_003198.1.

Genome annotation databases

EnsemblBacteriaiAAO67866; AAO67866; t0134.
CAD01287; CAD01287; CAD01287.
GeneIDi1246645.
KEGGisty:STY0150.
PATRICi18538116. VBISalEnt120419_0150.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL513382 Genomic DNA. Translation: CAD01287.1.
AE014613 Genomic DNA. Translation: AAO67866.1.
RefSeqiNP_454742.1. NC_003198.1.

3D structure databases

ProteinModelPortaliQ8Z9G7.
SMRiQ8Z9G7. Positions 1-306.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi220341.STY0150.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO67866; AAO67866; t0134.
CAD01287; CAD01287; CAD01287.
GeneIDi1246645.
KEGGisty:STY0150.
PATRICi18538116. VBISalEnt120419_0150.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiKYTEGFA.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: CT18.
  2. "Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18."
    Deng W., Liou S.-R., Plunkett G. III, Mayhew G.F., Rose D.J., Burland V., Kodoyianni V., Schwartz D.C., Blattner F.R.
    J. Bacteriol. 185:2330-2337(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700931 / Ty2.

Entry informationi

Entry nameiDDLB_SALTI
AccessioniPrimary (citable) accession number: Q8Z9G7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 100 of the entry and version 3 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.