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Q3JNE1

- DDL_BURP1

UniProt

Q3JNE1 - DDL_BURP1

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Burkholderia pseudomallei (strain 1710b)
Status
Reviewed - 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

BioCyciBPSE320372:GBYB-3542-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:BURPS1710b_3542
OrganismiBurkholderia pseudomallei (strain 1710b)
Taxonomic identifieri320372 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiapseudomallei group
ProteomesiUP000002700: Chromosome I

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 312312D-alanine--D-alanine ligasePRO_0000341076Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi320372.BURPS1710b_3542.

Structurei

Secondary structure

1
312
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
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 – 858Combined sources
Beta strandi89 – 924Combined sources
Helixi95 – 1028Combined sources
Helixi104 – 11411Combined sources
Beta strandi121 – 1255Combined sources
Helixi130 – 14112Combined sources
Beta strandi143 – 1497Combined sources
Beta strandi159 – 1613Combined sources
Helixi164 – 1663Combined sources
Helixi167 – 17711Combined sources
Beta strandi179 – 1857Combined sources
Beta strandi192 – 1987Combined sources
Beta strandi206 – 2083Combined sources
Beta strandi229 – 2313Combined sources
Helixi236 – 25217Combined sources
Beta strandi257 – 2659Combined 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
4EGQX-ray2.20A/B/C/D1-312[»]
ProteinModelPortaliQ3JNE1.
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.
OMAiKLAFQYD.
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]
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.
RefSeqiYP_334912.1. NC_007434.1.

Genome annotation databases

EnsemblBacteriaiABA49167; ABA49167; BURPS1710b_3542.
GeneIDi3690512.
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 .
RefSeqi YP_334912.1. NC_007434.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4EGQ X-ray 2.20 A/B/C/D 1-312 [» ]
ProteinModelPortali Q3JNE1.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 320372.BURPS1710b_3542.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABA49167 ; ABA49167 ; BURPS1710b_3542 .
GeneIDi 3690512.
KEGGi bpm:BURPS1710b_3542.
PATRICi 19239676. VBIBurPse115837_3687.

Phylogenomic databases

eggNOGi COG1181.
HOGENOMi HOG000011592.
KOi K01921.
OMAi KLAFQYD.
OrthoDBi EOG6ND0KB.

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci BPSE320372:GBYB-3542-MONOMER.

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPi MF_00047. Dala_Dala_lig.
InterProi IPR011761. 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 ]
PANTHERi PTHR23132. PTHR23132. 1 hit.
Pfami PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view ]
SUPFAMi SSF52440. SSF52440. 1 hit.
TIGRFAMsi TIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEi PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. Woods D.E., Nierman W.C.
    Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1710b.

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 26, 2014
This is version 72 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

External Data

Dasty 3