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B5ETW5

- DDL_VIBFM

UniProt

B5ETW5 - DDL_VIBFM

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Vibrio fischeri (strain MJ11)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi

Functioni

Cell wall formation.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 bindingi280 – 2801Magnesium or manganese 1UniRule annotation
Metal bindingi293 – 2931Magnesium or manganese 1UniRule annotation
Metal bindingi293 – 2931Magnesium or manganese 2UniRule annotation
Metal bindingi295 – 2951Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi150 – 20556ATPUniRule 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

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:VFMJ11_A0584
OrganismiVibrio fischeri (strain MJ11)
Taxonomic identifieri388396 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
ProteomesiUP000001857: Chromosome II

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 – 330330D-alanine--D-alanine ligasePRO_1000091214Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi388396.VFMJ11_A0584.

Structurei

3D structure databases

ProteinModelPortaliB5ETW5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 326207ATP-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.
OMAiRSAYGIY.
OrthoDBiEOG6ND0KB.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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. 1 hit.
[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.

B5ETW5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTHILLLCGG GGTEHEVSLV SSKYIAQQLS ELDAFDITHL EIKDEGWFHI
60 70 80 90 100
ESGLKYELRS DKTLLSGETV SSPVDYVVPC IHGYPGETGD IQSMLDMLSI
110 120 130 140 150
PYLGCDAESS TNSFNKITSK LWYDALGIPN TPYLFLTENN EETHQSALAA
160 170 180 190 200
FKQWGGLFVK AACQGSSVGC YKVTSEEELA QAINGAFGYS QQVLVEKAVK
210 220 230 240 250
PRELEVAAYE IDGQLFTTAP GEVTAPDGAF YTYDEKYGSG SHSTTSLDAQ
260 270 280 290 300
NLTEEQVKLI DQYSRKVFTQ MKLKDLSRID FFLTDDNEIY LNEVNTFPGM
310 320 330
TPISMFPKLL EHNGDCFKTF LQKAVLNAIK
Length:330
Mass (Da):36,565
Last modified:October 14, 2008 - v1
Checksum:iFA83FAF48D053079
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001133 Genomic DNA. Translation: ACH63474.1.
RefSeqiWP_012534691.1. NC_011186.1.
YP_002158133.1. NC_011186.1.

Genome annotation databases

EnsemblBacteriaiACH63474; ACH63474; VFMJ11_A0584.
GeneIDi6809225.
KEGGivfm:VFMJ11_A0584.
PATRICi20125420. VBIVibFis37164_3334.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP001133 Genomic DNA. Translation: ACH63474.1 .
RefSeqi WP_012534691.1. NC_011186.1.
YP_002158133.1. NC_011186.1.

3D structure databases

ProteinModelPortali B5ETW5.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 388396.VFMJ11_A0584.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACH63474 ; ACH63474 ; VFMJ11_A0584 .
GeneIDi 6809225.
KEGGi vfm:VFMJ11_A0584.
PATRICi 20125420. VBIVibFis37164_3334.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .

Family and domain databases

Gene3Di 3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
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. 1 hit.
[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 Vibrio fischeri strain MJ11."
    Mandel M.J., Stabb E.V., Ruby E.G., Ferriera S., Johnson J., Kravitz S., Beeson K., Sutton G., Rogers Y.-H., Friedman R., Frazier M., Venter J.C.
    Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: MJ11.

Entry informationi

Entry nameiDDL_VIBFM
AccessioniPrimary (citable) accession number: B5ETW5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 24, 2009
Last sequence update: October 14, 2008
Last modified: October 29, 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

Documents

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

External Data

Dasty 3