Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Leuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / NCDO 523)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 bindingi303 – 3031Magnesium or manganese 1UniRule annotation
Metal bindingi316 – 3161Magnesium or manganese 1UniRule annotation
Metal bindingi316 – 3161Magnesium or manganese 2UniRule annotation
Metal bindingi318 – 3181Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi170 – 22556ATPUniRule 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

BioCyciLMES203120:GJ8T-264-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:LEUM_0264
OrganismiLeuconostoc mesenteroides subsp. mesenteroides (strain ATCC 8293 / NCDO 523)
Taxonomic identifieri203120 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLeuconostocaceaeLeuconostoc
ProteomesiUP000000362 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 – 377377D-alanine--D-alanine ligasePRO_1000030463Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi203120.LEUM_0264.

Structurei

Secondary structure

1
377
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Helixi17 – 3418Combined sources
Beta strandi35 – 4410Combined sources
Helixi53 – 608Combined sources
Helixi65 – 739Combined sources
Helixi86 – 894Combined sources
Beta strandi95 – 1006Combined sources
Turni104 – 1063Combined sources
Beta strandi107 – 1093Combined sources
Helixi110 – 1178Combined sources
Beta strandi122 – 1243Combined sources
Helixi127 – 1348Combined sources
Helixi136 – 1449Combined sources
Turni145 – 1473Combined sources
Beta strandi153 – 1564Combined sources
Helixi160 – 1634Combined sources
Helixi166 – 1738Combined sources
Beta strandi177 – 1837Combined sources
Turni186 – 1894Combined sources
Beta strandi190 – 1934Combined sources
Helixi196 – 20611Combined sources
Turni207 – 2093Combined sources
Beta strandi213 – 2175Combined sources
Beta strandi224 – 23411Combined sources
Beta strandi236 – 2449Combined sources
Beta strandi248 – 2525Combined sources
Helixi257 – 2604Combined sources
Beta strandi268 – 2725Combined sources
Helixi277 – 29317Combined sources
Beta strandi298 – 3069Combined sources
Beta strandi312 – 3209Combined sources
Helixi328 – 3303Combined sources
Helixi332 – 3365Combined sources
Helixi340 – 36021Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EHIX-ray2.38A/B1-377[»]
ProteinModelPortaliQ03ZI1.
SMRiQ03ZI1. Positions 3-362.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ03ZI1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini140 – 349210ATP-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.

Q03ZI1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKKRVALIF GGNSSEHDVS KRSAQNFYNA IEATGKYEII VFAIAQNGFF
60 70 80 90 100
LDTESSKKIL ALEDEQPIVD AFMKTVDASD PLARIHALKS AGDFDIFFPV
110 120 130 140 150
VHGNLGEDGT LQGLFKLLDK PYVGAPLRGH AVSFDKALTK ELLTVNGIRN
160 170 180 190 200
TKYIVVDPES ANNWSWDKIV AELGNIVFVK AANQGSSVGI SRVTNAEEYT
210 220 230 240 250
EALSDSFQYD YKVLIEEAVN GARELEVGVI GNDQPLVSEI GAHTVPNQGS
260 270 280 290 300
GDGWYDYNNK FVDNSAVHFE IPAQLSPEVT KEVKQMALDA YKVLNLRGEA
310 320 330 340 350
RMDFLLDENN VPYLGEPNTL PGFTNMSLFK RLWDYSDINN AKLVDMLIDY
360 370
GFEDFAQNKK LSYSFVSLGE EKIGKFN
Length:377
Mass (Da):41,826
Last modified:November 14, 2006 - v1
Checksum:iD1C6A40A6812AE01
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000414 Genomic DNA. Translation: ABJ61391.1.
RefSeqiWP_011679162.1. NC_008531.1.
YP_817764.1. NC_008531.1.

Genome annotation databases

EnsemblBacteriaiABJ61391; ABJ61391; LEUM_0264.
KEGGilme:LEUM_0264.
PATRICi22408513. VBILeuMes50664_0271.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000414 Genomic DNA. Translation: ABJ61391.1.
RefSeqiWP_011679162.1. NC_008531.1.
YP_817764.1. NC_008531.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EHIX-ray2.38A/B1-377[»]
ProteinModelPortaliQ03ZI1.
SMRiQ03ZI1. Positions 3-362.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi203120.LEUM_0264.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABJ61391; ABJ61391; LEUM_0264.
KEGGilme:LEUM_0264.
PATRICi22408513. VBILeuMes50664_0271.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011593.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciLMES203120:GJ8T-264-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ03ZI1.

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: ATCC 8293 / NCDO 523.

Entry informationi

Entry nameiDDL_LEUMM
AccessioniPrimary (citable) accession number: Q03ZI1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: November 14, 2006
Last modified: June 24, 2015
This is version 71 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.