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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Burkholderia xenovorans (strain LB400)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi262 – 2621Magnesium or manganese 1UniRule annotation
Metal bindingi275 – 2751Magnesium or manganese 1UniRule annotation
Metal bindingi275 – 2751Magnesium or manganese 2UniRule annotation
Metal bindingi277 – 2771Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi138 – 19356ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. D-alanine-D-alanine ligase activity Source: UniProtKB-HAMAP
  3. magnesium ion binding Source: UniProtKB-HAMAP
  4. manganese ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  3. regulation of cell shape Source: UniProtKB-KW
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

BioCyciBXEN266265:GJII-4063-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:Bxeno_A3907
ORF Names:Bxe_A0488
OrganismiBurkholderia xenovorans (strain LB400)
Taxonomic identifieri266265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderia
ProteomesiUP000001817 Componenti: Chromosome 1

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 313313D-alanine--D-alanine ligasePRO_0000341080Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi266265.Bxe_A0488.

Structurei

Secondary structure

1
313
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 94Combined sources
Beta strandi11 – 155Combined sources
Helixi23 – 3917Combined sources
Beta strandi43 – 475Combined sources
Turni49 – 513Combined sources
Helixi56 – 594Combined sources
Beta strandi64 – 674Combined sources
Helixi72 – 743Combined sources
Helixi78 – 869Combined sources
Beta strandi89 – 924Combined sources
Helixi95 – 1017Combined sources
Helixi104 – 11310Combined sources
Beta strandi121 – 1255Combined sources
Helixi130 – 14112Combined sources
Beta strandi143 – 1497Combined sources
Helixi164 – 1663Combined sources
Helixi167 – 1748Combined sources
Turni175 – 1773Combined sources
Beta strandi179 – 1857Combined sources
Beta strandi189 – 19810Combined sources
Beta strandi206 – 2083Combined sources
Beta strandi228 – 2314Combined sources
Helixi236 – 25116Combined sources
Turni252 – 2543Combined sources
Beta strandi257 – 26610Combined sources
Beta strandi271 – 2799Combined sources
Helixi287 – 2948Combined sources
Helixi299 – 30810Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EGJX-ray2.30A/B/C/D1-313[»]
ProteinModelPortaliQ13TZ4.
SMRiQ13TZ4. Positions 10-309.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 308201ATP-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.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

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. 2 hits.
[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.

Q13TZ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSIDPKQFG KVAVLLGGNS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA
60 70 80 90 100
ERPLAALKEE GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL
110 120 130 140 150
GLDKFRTKLV WQQLGIPTPP FEAVLRGDDY EARAKEIVAK LGLPLFVKPA
160 170 180 190 200
SEGSSVAVIK VKSADALPAA LIEAVKFDRI VVVEKSIEGG GEYTACIAGN
210 220 230 240 250
LDLPVIRIVP AGEFYDYHAK YIANDTQYLI PCGLTADEEA RLKVLARRAF
260 270 280 290 300
DVLGCTDWGR ADFMLDADGN PYFLEVNTAP GMTDHSLPPK AARAVGISYQ
310
ELVVAVLALT LKD
Length:313
Mass (Da):33,535
Last modified:August 22, 2006 - v1
Checksum:iDDBB5D2E458BD6D3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000270 Genomic DNA. Translation: ABE32445.1.
RefSeqiYP_560497.1. NC_007951.1.

Genome annotation databases

EnsemblBacteriaiABE32445; ABE32445; Bxe_A0488.
KEGGibxe:Bxe_A0488.
PATRICi19333671. VBIBurXen52548_4128.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000270 Genomic DNA. Translation: ABE32445.1.
RefSeqiYP_560497.1. NC_007951.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EGJX-ray2.30A/B/C/D1-313[»]
ProteinModelPortaliQ13TZ4.
SMRiQ13TZ4. Positions 10-309.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266265.Bxe_A0488.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABE32445; ABE32445; Bxe_A0488.
KEGGibxe:Bxe_A0488.
PATRICi19333671. VBIBurXen52548_4128.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciBXEN266265:GJII-4063-MONOMER.

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. 2 hits.
[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: LB400.

Entry informationi

Entry nameiDDL_BURXL
AccessioniPrimary (citable) accession number: Q13TZ4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: August 22, 2006
Last modified: April 1, 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.