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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Burkholderia ambifaria (strain MC40-6)
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 bindingi262Magnesium or manganese 1UniRule annotation1
Metal bindingi275Magnesium or manganese 1UniRule annotation1
Metal bindingi275Magnesium or manganese 2UniRule annotation1
Metal bindingi277Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi138 – 193ATPUniRule 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:BamMC406_0490
OrganismiBurkholderia ambifaria (strain MC40-6)
Taxonomic identifieri398577 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex
Proteomesi
  • UP000001680 Componenti: Chromosome 1

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_10000911641 – 313D-alanine--D-alanine ligaseAdd BLAST313

Structurei

Secondary structure

1313
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 9Combined sources4
Beta strandi11 – 15Combined sources5
Helixi23 – 39Combined sources17
Beta strandi43 – 47Combined sources5
Turni49 – 51Combined sources3
Helixi56 – 59Combined sources4
Beta strandi64 – 67Combined sources4
Helixi72 – 74Combined sources3
Helixi78 – 86Combined sources9
Beta strandi89 – 92Combined sources4
Helixi95 – 102Combined sources8
Helixi104 – 113Combined sources10
Beta strandi121 – 125Combined sources5
Helixi130 – 141Combined sources12
Beta strandi145 – 149Combined sources5
Beta strandi159 – 161Combined sources3
Helixi164 – 166Combined sources3
Helixi167 – 174Combined sources8
Turni175 – 177Combined sources3
Beta strandi179 – 185Combined sources7
Beta strandi189 – 198Combined sources10
Beta strandi206 – 209Combined sources4
Helixi211 – 213Combined sources3
Beta strandi227 – 231Combined sources5
Helixi236 – 251Combined sources16
Turni252 – 254Combined sources3
Beta strandi257 – 265Combined sources9
Beta strandi271 – 279Combined sources9
Helixi287 – 294Combined sources8
Helixi299 – 308Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EG0X-ray1.65A/B1-313[»]
ProteinModelPortaliB1YSS6.
SMRiB1YSS6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini108 – 308ATP-graspUniRule annotationAdd BLAST201

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiFQHDDEV.
OrthoDBiPOG091H00GT.

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.

B1YSS6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGIDPKRFG KVAVLFGGES AEREVSLTSG RLVLQGLRDA GIDAHPFDPA
60 70 80 90 100
ERPLSALKDE GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL
110 120 130 140 150
GLDKFRTKLV WQQTGVPTPP FETVMRGDDY AARATDIVAK LGLPLFVKPA
160 170 180 190 200
SEGSSVAVLK VKTADALPAA LSEAATHDKI VIVEKSIEGG GEYTACIAGD
210 220 230 240 250
LDLPLIKIVP AGEFYDYHAK YVANDTQYLI PCGLPAEQET ELKRIARRAF
260 270 280 290 300
DVLGCTDWGR ADFMLDAAGN AYFLEVNTAP GMTDHSLPPK AARSIGIGYS
310
ELVVKVLSLT LND
Length:313
Mass (Da):33,393
Last modified:May 20, 2008 - v1
Checksum:i494D539CF13A281A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001025 Genomic DNA. Translation: ACB62987.1.
RefSeqiWP_012363028.1. NC_010551.1.

Genome annotation databases

EnsemblBacteriaiACB62987; ACB62987; BamMC406_0490.
KEGGibac:BamMC406_0490.
PATRICi19030268. VBIBurAmb82852_0485.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001025 Genomic DNA. Translation: ACB62987.1.
RefSeqiWP_012363028.1. NC_010551.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EG0X-ray1.65A/B1-313[»]
ProteinModelPortaliB1YSS6.
SMRiB1YSS6.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACB62987; ACB62987; BamMC406_0490.
KEGGibac:BamMC406_0490.
PATRICi19030268. VBIBurAmb82852_0485.

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiFQHDDEV.
OrthoDBiPOG091H00GT.

Enzyme and pathway databases

UniPathwayiUPA00219.

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_BURA4
AccessioniPrimary (citable) accession number: B1YSS6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: May 20, 2008
Last modified: November 2, 2016
This is version 61 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

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.