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Protein

D-alanine--D-alanine ligase

Gene

ddlB

Organism
Escherichia coli (strain K12 / MC4100 / BW2952)
Status
Unreviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Cell wall formation.UniRule annotationSAAS annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationSAAS annotation, Mn2+UniRule annotationSAAS annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotationSAAS annotation

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei97 – 971ADPCombined sources
Binding sitei97 – 971ATPCombined sources
Binding sitei144 – 1441ADPCombined sources
Binding sitei144 – 1441ATPCombined sources
Binding sitei151 – 1511ADP; via amide nitrogenCombined sources
Binding sitei187 – 1871ADPCombined sources
Binding sitei187 – 1871ATPCombined sources
Binding sitei210 – 2101ADP; via amide nitrogenCombined sources
Binding sitei210 – 2101ATP; via amide nitrogenCombined sources
Binding sitei215 – 2151ADPCombined sources
Binding sitei215 – 2151ATPCombined sources
Metal bindingi257 – 2571Magnesium or manganese 1UniRule annotation
Binding sitei257 – 2571ADPCombined sources
Metal bindingi270 – 2701MagnesiumCombined sources
Metal bindingi270 – 2701Magnesium or manganese 1UniRule annotation
Metal bindingi270 – 2701Magnesium or manganese 2UniRule annotation
Binding sitei270 – 2701ADPCombined sources
Metal bindingi272 – 2721MagnesiumCombined sources
Metal bindingi272 – 2721Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi134 – 18956ATPUniRule annotationAdd
BLAST
Nucleotide bindingi150 – 1512ATPCombined sources
Nucleotide bindingi180 – 1834ADPCombined sources
Nucleotide bindingi180 – 1834ATPCombined sources
Nucleotide bindingi255 – 2573ATPCombined sources
Nucleotide bindingi270 – 2723ATPCombined sources

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 annotationCombined sources, MagnesiumCombined sources, ManganeseUniRule annotationSAAS annotation, Metal-bindingCombined sources, Nucleotide-binding

Enzyme and pathway databases

BioCyciECOL595496:GI18-90-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:ddlBImported
Synonyms:ddlUniRule annotation
Ordered Locus Names:BWG_0087Imported
OrganismiEscherichia coli (strain K12 / MC4100 / BW2952)Imported
Taxonomic identifieri595496 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000001478 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

PTM / Processingi

Proteomic databases

PRIDEiC4ZRI7.

Interactioni

Protein-protein interaction databases

STRINGi595496.BWG_0087.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C5AX-ray1.65A/B1-306[»]
4C5BX-ray1.50A/B1-306[»]
4C5CX-ray1.40A/B1-306[»]
ProteinModelPortaliC4ZRI7.
SMRiC4ZRI7. Positions 1-306.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

C4ZRI7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL
60 70 80 90 100
KSMGFQKVFI ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS
110 120 130 140 150
KLLWQGAGLP VAPWVALTRA EFEKGLSDKQ LAEISALGLP VIVKPSREGS
160 170 180 190 200
SVGMSKVVAE NALQDALRLA FQHDEEVLIE KWLSGPEFTV AILGEEILPS
210 220 230 240 250
IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL VLKAWTTLGC
260 270 280 290 300
KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR

ILELAD
Length:306
Mass (Da):32,840
Last modified:July 27, 2009 - v1
Checksum:iF2D401C323A04471
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001396 Genomic DNA. Translation: ACR62724.1.
RefSeqiYP_002925289.1. NC_012759.1.

Genome annotation databases

EnsemblBacteriaiACR62724; ACR62724; BWG_0087.
KEGGiebw:BWG_0087.
PATRICi18269066. VBIEscCol60876_0097.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001396 Genomic DNA. Translation: ACR62724.1.
RefSeqiYP_002925289.1. NC_012759.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C5AX-ray1.65A/B1-306[»]
4C5BX-ray1.50A/B1-306[»]
4C5CX-ray1.40A/B1-306[»]
ProteinModelPortaliC4ZRI7.
SMRiC4ZRI7. Positions 1-306.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi595496.BWG_0087.

Proteomic databases

PRIDEiC4ZRI7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACR62724; ACR62724; BWG_0087.
KEGGiebw:BWG_0087.
PATRICi18269066. VBIEscCol60876_0097.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiKYTEGFA.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
UPA00219.
BioCyciECOL595496:GI18-90-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. 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

« Hide 'large scale' publications
  1. "Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12."
    Ferenci T., Zhou Z., Betteridge T., Ren Y., Liu Y., Feng L., Reeves P.R., Wang L.
    J. Bacteriol. 191:4025-4029(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MC4100 / BW2952Imported.
  2. "D-Cycloserine Inhibition Occurs by a Novel Phosphoryl Intermediate: Prospects for Novel Antimicrobials without Psychotic Side Effects."
    Batson S., Majce V., Lloyd A.J., Rea D., Fishwick C.W.G., Simmons K.J., Fulop V., Roper D.I.
    Submitted (AUG-2013) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) IN COMPLEX WITH ATP AND MAGNESIUM.

Entry informationi

Entry nameiC4ZRI7_ECOBW
AccessioniPrimary (citable) accession number: C4ZRI7
Entry historyi
Integrated into UniProtKB/TrEMBL: July 27, 2009
Last sequence update: July 27, 2009
Last modified: March 31, 2015
This is version 43 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete 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.