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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Burkholderia pseudomallei (strain 1710b)
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:BURPS1710b_3542
OrganismiBurkholderia pseudomallei (strain 1710b)
Taxonomic identifieri320372 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiapseudomallei group
Proteomesi
  • UP000002700 Componenti: Chromosome I

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_00003410761 – 312D-alanine--D-alanine ligaseAdd BLAST312

Structurei

Secondary structure

1312
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
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 – 85Combined sources8
Beta strandi89 – 92Combined sources4
Helixi95 – 102Combined sources8
Helixi104 – 114Combined sources11
Beta strandi121 – 125Combined sources5
Helixi130 – 141Combined sources12
Beta strandi143 – 149Combined sources7
Beta strandi159 – 161Combined sources3
Helixi164 – 166Combined sources3
Helixi167 – 177Combined sources11
Beta strandi179 – 185Combined sources7
Beta strandi192 – 198Combined sources7
Beta strandi206 – 208Combined sources3
Beta strandi229 – 231Combined sources3
Helixi236 – 252Combined sources17
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
4EGQX-ray2.20A/B/C/D1-312[»]
ProteinModelPortaliQ3JNE1.
SMRiQ3JNE1.
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.

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.

Q3JNE1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGIDPKRFG KVAVLLGGDS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA
60 70 80 90 100
QRPLAALKDE GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL
110 120 130 140 150
GLDKFRTKLV WQQTGIPTPP FETVMRGDDY AARAQDIVAK LGVPLFVKPA
160 170 180 190 200
SEGSSVAVEK VKSADALPAA LEEAAKHDKI VIVEKSIEGG GEYTACIAAD
210 220 230 240 250
LDLPLIRIVP AGEFYDYHAK YIANDTQYLI PCGLDAAKEA EFKRIARRAF
260 270 280 290 300
DVLGCTDWGR ADFMLDAAGN PYFLEVNTAP GMTDHSLPPK AARAVGIGYS
310
ELVVKVLSLT LD
Length:312
Mass (Da):33,341
Last modified:November 8, 2005 - v1
Checksum:iCCD89397BEAE5E22
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000124 Genomic DNA. Translation: ABA49167.1.
RefSeqiWP_004194254.1. NC_007434.1.

Genome annotation databases

EnsemblBacteriaiABA49167; ABA49167; BURPS1710b_3542.
KEGGibpm:BURPS1710b_3542.
PATRICi19239676. VBIBurPse115837_3687.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000124 Genomic DNA. Translation: ABA49167.1.
RefSeqiWP_004194254.1. NC_007434.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EGQX-ray2.20A/B/C/D1-312[»]
ProteinModelPortaliQ3JNE1.
SMRiQ3JNE1.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA49167; ABA49167; BURPS1710b_3542.
KEGGibpm:BURPS1710b_3542.
PATRICi19239676. VBIBurPse115837_3687.

Phylogenomic databases

HOGENOMiHOG000011592.
KOiK01921.
OMAiFQHDDEV.

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_BURP1
AccessioniPrimary (citable) accession number: Q3JNE1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: November 8, 2005
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

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.