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B5YFT1

- DDL_THEYD

UniProt

B5YFT1 - DDL_THEYD

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Protein
D-alanine--D-alanine ligase
Gene
ddl, THEYE_A1319
Organism
Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)
Status
Reviewed - Annotation score: 3 out of 5 - Protein inferred from homologyi

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 bindingi250 – 2501Magnesium or manganese 1 By similarity
Metal bindingi263 – 2631Magnesium or manganese 1 By similarity
Metal bindingi263 – 2631Magnesium or manganese 2 By similarity
Metal bindingi265 – 2651Magnesium or manganese 2 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi127 – 18256ATP 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
Complete GO annotation...

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

BioCyciTYEL289376:GH9L-1311-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:THEYE_A1319
OrganismiThermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)
Taxonomic identifieri289376 [NCBI]
Taxonomic lineageiBacteriaNitrospiraeNitrospiralesNitrospiraceaeThermodesulfovibrio
ProteomesiUP000000718: Chromosome

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 – 304304D-alanine--D-alanine ligaseUniRule annotation
PRO_1000091212Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi289376.THEYE_A1319.

Structurei

3D structure databases

ProteinModelPortaliB5YFT1.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini99 – 296198ATP-grasp
Add
BLAST

Sequence similaritiesi

Contains 1 ATP-grasp domain.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiANDTQYR.
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.

B5YFT1-1 [UniParc]FASTAAdd to Basket

« Hide

MKVGVIAGGI SSEREVSLRS GQAVFNALKE LGYDVVFIDA GIDLCEKIKI    50
EKIDIAFLVL HGGWGENGAV QGMLEVMGIP YTGSGVLASA LAMDKEASKK 100
IFLYHGIPVP PFKVLNKKDY ISSAVSLSSF SFPCVVKPAE EGSSIGVNIV 150
KNEREFKNAI NEAFQFGKRV IIEKFIEGRE IHIGVLGDKA LGGVEVRPKK 200
GFYSYEAKYT KGLTEYILPP EIDNALYEKL KELGLKAHKS LNCKGGTRVD 250
MIVDQQGNPY VLEVNTIPGM TETSLLPKIA SLAGYDFKGL VKEILELSLK 300
NNEK 304
Length:304
Mass (Da):33,164
Last modified:November 25, 2008 - v1
Checksum:i1603183954A06AF8
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001147 Genomic DNA. Translation: ACI21742.1.
RefSeqiYP_002249129.1. NC_011296.1.

Genome annotation databases

EnsemblBacteriaiACI21742; ACI21742; THEYE_A1319.
GeneIDi6941962.
KEGGitye:THEYE_A1319.
PATRICi23909657. VBITheYel104483_1286.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001147 Genomic DNA. Translation: ACI21742.1 .
RefSeqi YP_002249129.1. NC_011296.1.

3D structure databases

ProteinModelPortali B5YFT1.
ModBasei Search...

Protein-protein interaction databases

STRINGi 289376.THEYE_A1319.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACI21742 ; ACI21742 ; THEYE_A1319 .
GeneIDi 6941962.
KEGGi tye:THEYE_A1319.
PATRICi 23909657. VBITheYel104483_1286.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci TYEL289376:GH9L-1311-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. "The complete genome sequence of Thermodesulfovibrio yellowstonii strain ATCC 51303 / DSM 11347 / YP87."
    Dodson R.J., Durkin A.S., Wu M., Eisen J., Sutton G.
    Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51303 / DSM 11347 / YP87.

Entry informationi

Entry nameiDDL_THEYD
AccessioniPrimary (citable) accession number: B5YFT1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: November 25, 2008
Last modified: May 14, 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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