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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
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 bindingi289Magnesium or manganese 1UniRule annotation1
Metal bindingi302Magnesium or manganese 1UniRule annotation1
Metal bindingi302Magnesium or manganese 2UniRule annotation1
Metal bindingi304Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi163 – 218ATPUniRule 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:SMU_599
OrganismiStreptococcus mutans serotype c (strain ATCC 700610 / UA159)
Taxonomic identifieri210007 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000002512 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_00001778861 – 349D-alanine--D-alanine ligaseAdd BLAST349

Interactioni

Protein-protein interaction databases

STRINGi210007.SMU_599.

Structurei

Secondary structure

1349
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 11Combined sources8
Helixi17 – 30Combined sources14
Turni33 – 35Combined sources3
Beta strandi36 – 43Combined sources8
Beta strandi49 – 57Combined sources9
Helixi73 – 75Combined sources3
Helixi79 – 82Combined sources4
Beta strandi88 – 92Combined sources5
Turni96 – 98Combined sources3
Beta strandi99 – 101Combined sources3
Helixi102 – 109Combined sources8
Beta strandi114 – 116Combined sources3
Helixi119 – 126Combined sources8
Helixi128 – 138Combined sources11
Beta strandi146 – 150Combined sources5
Helixi155 – 165Combined sources11
Beta strandi168 – 174Combined sources7
Beta strandi184 – 188Combined sources5
Helixi189 – 202Combined sources14
Beta strandi204 – 210Combined sources7
Beta strandi214 – 226Combined sources13
Beta strandi233 – 235Combined sources3
Beta strandi255 – 258Combined sources4
Helixi263 – 279Combined sources17
Beta strandi284 – 292Combined sources9
Beta strandi298 – 306Combined sources9
Helixi314 – 321Combined sources8
Helixi326 – 345Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3K3PX-ray2.23A/B1-349[»]
ProteinModelPortaliP95803.
SMRiP95803.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP95803.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini133 – 335ATP-graspUniRule annotationAdd BLAST203

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.
KOiK01921.
OMAiWITDEES.
PhylomeDBiP95803.

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. 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.

P95803-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKETLVLLY GGRSAERDVS VLSAESVMRA INYDNFLVKT YFITQAGDFI
60 70 80 90 100
KTQEFDSQPS ETDKLMTNDT IIASQKIKPS DIYEEEAVVF PVLHGPMGED
110 120 130 140 150
GSIQGFLEVL KMPYVGTNIL SSSVAMDKIT TNQVLESATT IPQVAYVALI
160 170 180 190 200
EGEPLESKLA EVEEKLIYPV FVKPANMGSS VGISKAENRT DLKQAIALAL
210 220 230 240 250
KYDSRVLIEQ GVDAREIEVG ILGNTDVKTT LPGEIVKDVA FYDYEAKYID
260 270 280 290 300
NKITMAIPAE IDPVIVEKMR DYAATAFRTL GCCGLSRCDF FLTEDGKVYL
310 320 330 340
NELNTMPGFT QWSMYPLLWE NMGLSYSVLI EELVSLAKEM FDKRESHLV
Length:349
Mass (Da):38,838
Last modified:November 28, 2002 - v2
Checksum:iFFDAAD9942CAE7EF
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti132N → K in AAB41854 (Ref. 2) Curated1
Sequence conflicti238D → V in AAB41854 (Ref. 2) Curated1
Sequence conflicti273A → R in AAB41854 (Ref. 2) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014133 Genomic DNA. Translation: AAN58338.1.
U69165 Genomic DNA. Translation: AAB41854.1.
RefSeqiNP_721032.1. NC_004350.2.
WP_002352219.1. NC_004350.2.

Genome annotation databases

EnsemblBacteriaiAAN58338; AAN58338; SMU_599.
GeneIDi1029384.
KEGGismu:SMU_599.
PATRICi19663399. VBIStrMut61772_0532.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014133 Genomic DNA. Translation: AAN58338.1.
U69165 Genomic DNA. Translation: AAB41854.1.
RefSeqiNP_721032.1. NC_004350.2.
WP_002352219.1. NC_004350.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3K3PX-ray2.23A/B1-349[»]
ProteinModelPortaliP95803.
SMRiP95803.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi210007.SMU_599.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN58338; AAN58338; SMU_599.
GeneIDi1029384.
KEGGismu:SMU_599.
PATRICi19663399. VBIStrMut61772_0532.

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
KOiK01921.
OMAiWITDEES.
PhylomeDBiP95803.

Enzyme and pathway databases

UniPathwayiUPA00219.

Miscellaneous databases

EvolutionaryTraceiP95803.

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. 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_STRMU
AccessioniPrimary (citable) accession number: P95803
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 28, 2002
Last modified: November 2, 2016
This is version 121 of the entry and version 2 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.