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B1YSS6

- DDL_BURA4

UniProt

B1YSS6 - DDL_BURA4

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Protein
D-alanine--D-alanine ligase
Gene
ddl, BamMC406_0490
Organism
Burkholderia ambifaria (strain MC40-6)
Status
Reviewed - Annotation score: 3 out of 5 - Experimental evidence at protein leveli

Functioni

Cell wall formation By similarity.UniRule annotation

Catalytic activityi

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine.UniRule annotation

Cofactori

Binds 2 magnesium or manganese ions per subunit By similarity.

Pathwayi

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi138 – 19356ATP By similarity
Add
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. peptidoglycan biosynthetic process Source: UniProtKB-HAMAP
  2. 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

BioCyciBAMB398577:GH38-510-MONOMER.
UniPathwayiUPA00219.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanine--D-alanine ligase (EC:6.3.2.4)
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene namesi
Name:ddl
Ordered Locus Names:BamMC406_0490
OrganismiBurkholderia ambifaria (strain MC40-6)
Taxonomic identifieri398577 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiaBurkholderia cepacia complex
ProteomesiUP000001680: Chromosome 1

Subcellular locationi

Cytoplasm By similarity 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 ligaseUniRule annotation
PRO_1000091164Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi398577.BamMC406_0490.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 94
Beta strandi11 – 155
Helixi23 – 3917
Beta strandi43 – 475
Turni49 – 513
Helixi56 – 594
Beta strandi64 – 674
Helixi72 – 743
Helixi78 – 869
Beta strandi89 – 924
Helixi95 – 1028
Helixi104 – 11310
Beta strandi121 – 1255
Helixi130 – 14112
Beta strandi145 – 1495
Beta strandi159 – 1613
Helixi164 – 1663
Helixi167 – 1748
Turni175 – 1773
Beta strandi179 – 1857
Beta strandi189 – 19810
Beta strandi206 – 2094
Beta strandi227 – 2315
Helixi236 – 25116
Turni252 – 2543
Beta strandi257 – 2659
Beta strandi271 – 2799
Helixi287 – 2948
Helixi299 – 30810

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4EG0X-ray1.65A/B1-313[»]
ProteinModelPortaliB1YSS6.
SMRiB1YSS6. Positions 10-309.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 308201ATP-grasp
Add
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

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.

B1YSS6-1 [UniParc]FASTAAdd to Basket

« Hide

MSGIDPKRFG KVAVLFGGES AEREVSLTSG RLVLQGLRDA GIDAHPFDPA    50
ERPLSALKDE GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL 100
GLDKFRTKLV WQQTGVPTPP FETVMRGDDY AARATDIVAK LGLPLFVKPA 150
SEGSSVAVLK VKTADALPAA LSEAATHDKI VIVEKSIEGG GEYTACIAGD 200
LDLPLIKIVP AGEFYDYHAK YVANDTQYLI PCGLPAEQET ELKRIARRAF 250
DVLGCTDWGR ADFMLDAAGN AYFLEVNTAP GMTDHSLPPK AARSIGIGYS 300
ELVVKVLSLT LND 313
Length:313
Mass (Da):33,393
Last modified:May 20, 2008 - v1
Checksum:i494D539CF13A281A
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001025 Genomic DNA. Translation: ACB62987.1.
RefSeqiWP_012363028.1. NC_010551.1.
YP_001807203.1. NC_010551.1.

Genome annotation databases

EnsemblBacteriaiACB62987; ACB62987; BamMC406_0490.
GeneIDi6177804.
KEGGibac:BamMC406_0490.
PATRICi19030268. VBIBurAmb82852_0485.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001025 Genomic DNA. Translation: ACB62987.1 .
RefSeqi WP_012363028.1. NC_010551.1.
YP_001807203.1. NC_010551.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4EG0 X-ray 1.65 A/B 1-313 [» ]
ProteinModelPortali B1YSS6.
SMRi B1YSS6. Positions 10-309.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 398577.BamMC406_0490.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACB62987 ; ACB62987 ; BamMC406_0490 .
GeneIDi 6177804.
KEGGi bac:BamMC406_0490.
PATRICi 19030268. VBIBurAmb82852_0485.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci BAMB398577:GH38-510-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. "Complete sequence of chromosome 1 of Burkholderia ambifaria MC40-6."
    Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A.
    , Ramette A., Konstantinidis K., Tiedje J., Richardson P.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MC40-6.

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: September 3, 2014
This is version 46 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

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