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

Pathwayi: 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)DescriptionActionsGraphical viewLength
Metal bindingi303Magnesium or manganese 1UniRule annotation1
Metal bindingi316Magnesium or manganese 1UniRule annotation1
Metal bindingi316Magnesium or manganese 2UniRule annotation1
Metal bindingi318Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi170 – 225ATPUniRule annotationAdd BLAST56

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 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
Proteomesi
  • UP000000362 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000304631 – 377D-alanine--D-alanine ligaseAdd BLAST377

Interactioni

Protein-protein interaction databases

STRINGi203120.LEUM_0264.

Structurei

Secondary structure

1377
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Helixi17 – 34Combined sources18
Beta strandi35 – 44Combined sources10
Helixi53 – 60Combined sources8
Helixi65 – 73Combined sources9
Helixi86 – 89Combined sources4
Beta strandi95 – 100Combined sources6
Turni104 – 106Combined sources3
Beta strandi107 – 109Combined sources3
Helixi110 – 117Combined sources8
Beta strandi122 – 124Combined sources3
Helixi127 – 134Combined sources8
Helixi136 – 144Combined sources9
Turni145 – 147Combined sources3
Beta strandi153 – 156Combined sources4
Helixi160 – 163Combined sources4
Helixi166 – 173Combined sources8
Beta strandi177 – 183Combined sources7
Turni186 – 189Combined sources4
Beta strandi190 – 193Combined sources4
Helixi196 – 206Combined sources11
Turni207 – 209Combined sources3
Beta strandi213 – 217Combined sources5
Beta strandi224 – 234Combined sources11
Beta strandi236 – 244Combined sources9
Beta strandi248 – 252Combined sources5
Helixi257 – 260Combined sources4
Beta strandi268 – 272Combined sources5
Helixi277 – 293Combined sources17
Beta strandi298 – 306Combined sources9
Beta strandi312 – 320Combined sources9
Helixi328 – 330Combined sources3
Helixi332 – 336Combined sources5
Helixi340 – 360Combined sources21

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ03ZI1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini140 – 349ATP-graspUniRule annotationAdd BLAST210

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
OrthoDBiPOG091H06GK.

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. 1 hit.
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]
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.

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1EHIX-ray2.38A/B1-377[»]
ProteinModelPortaliQ03ZI1.
SMRiQ03ZI1.
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

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011593.
KOiK01921.
OMAiMDKIAMK.
OrthoDBiPOG091H06GK.

Enzyme and pathway databases

UniPathwayiUPA00219.

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. 1 hit.
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]
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...

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: November 2, 2016
This is version 81 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

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 one 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.