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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

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 bindingi289 – 2891Magnesium or manganese 1UniRule annotation
Metal bindingi302 – 3021Magnesium or manganese 1UniRule annotation
Metal bindingi302 – 3021Magnesium or manganese 2UniRule annotation
Metal bindingi304 – 3041Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi163 – 21856ATPUniRule 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

BioCyciSMUT210007:GC7Z-588-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:SMU_599
OrganismiStreptococcus mutans serotype c (strain ATCC 700610 / UA159)
Taxonomic identifieri210007 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
ProteomesiUP000002512 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 – 349349D-alanine--D-alanine ligasePRO_0000177886Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi210007.SMU_599.

Structurei

Secondary structure

1
349
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 118Combined sources
Helixi17 – 3014Combined sources
Turni33 – 353Combined sources
Beta strandi36 – 438Combined sources
Beta strandi49 – 579Combined sources
Helixi73 – 753Combined sources
Helixi79 – 824Combined sources
Beta strandi88 – 925Combined sources
Turni96 – 983Combined sources
Beta strandi99 – 1013Combined sources
Helixi102 – 1098Combined sources
Beta strandi114 – 1163Combined sources
Helixi119 – 1268Combined sources
Helixi128 – 13811Combined sources
Beta strandi146 – 1505Combined sources
Helixi155 – 16511Combined sources
Beta strandi168 – 1747Combined sources
Beta strandi184 – 1885Combined sources
Helixi189 – 20214Combined sources
Beta strandi204 – 2107Combined sources
Beta strandi214 – 22613Combined sources
Beta strandi233 – 2353Combined sources
Beta strandi255 – 2584Combined sources
Helixi263 – 27917Combined sources
Beta strandi284 – 2929Combined sources
Beta strandi298 – 3069Combined sources
Helixi314 – 3218Combined sources
Helixi326 – 34520Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP95803.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini133 – 335203ATP-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.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.
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.
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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti132 – 1321N → K in AAB41854 (Ref. 2) Curated
Sequence conflicti238 – 2381D → V in AAB41854 (Ref. 2) Curated
Sequence conflicti273 – 2731A → R in AAB41854 (Ref. 2) Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
3K3PX-ray2.23A/B1-349[»]
ProteinModelPortaliP95803.
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

eggNOGiCOG1181.
KOiK01921.
OMAiWFPILHG.
OrthoDBiEOG64BQ73.
PhylomeDBiP95803.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciSMUT210007:GC7Z-588-MONOMER.

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.
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

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700610 / UA159.
  2. Garnier F., Gerbaud G., Courvalin P., Galimand M.
    Submitted (FEB-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 106-303.
    Strain: ATCC 25175 / DSM 20523 / JCM 5705 / NBRC 13955 / NCIMB 702062 / NCTC 10449.

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: June 24, 2015
This is version 117 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

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.