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Q5E006

- DDL_VIBF1

UniProt

Q5E006 - DDL_VIBF1

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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Vibrio fischeri (strain ATCC 700601 / ES114)
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

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 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

BioCyciAFIS312309:GIWP-3319-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:VF_A0570
OrganismiVibrio fischeri (strain ATCC 700601 / ES114)
Taxonomic identifieri312309 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
ProteomesiUP000000537: 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_0000341194Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi312309.VF_A0570.

Structurei

3D structure databases

ProteinModelPortaliQ5E006.
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.
OMAiGHILANI.
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.

Q5E006-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MTHILLLCGG GGTEHEVSLV SSKYISQQLS ELDAFEITHL 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 YKVTSEAELS KAINDAFGYS 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):36,611
Last modified:March 15, 2005 - v1
Checksum:iF0CED8F4D9AA04F5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000021 Genomic DNA. Translation: AAW87640.1.
RefSeqiYP_206528.1. NC_006841.2.

Genome annotation databases

EnsemblBacteriaiAAW87640; AAW87640; VF_A0570.
GeneIDi3280446.
KEGGivfi:VF_A0570.
PATRICi20117143. VBIVibFis127983_3176.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000021 Genomic DNA. Translation: AAW87640.1 .
RefSeqi YP_206528.1. NC_006841.2.

3D structure databases

ProteinModelPortali Q5E006.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 312309.VF_A0570.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAW87640 ; AAW87640 ; VF_A0570 .
GeneIDi 3280446.
KEGGi vfi:VF_A0570.
PATRICi 20117143. VBIVibFis127983_3176.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayi UPA00219 .
BioCyci AFIS312309:GIWP-3319-MONOMER.

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700601 / ES114.

Entry informationi

Entry nameiDDL_VIBF1
AccessioniPrimary (citable) accession number: Q5E006
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: March 15, 2005
Last modified: November 26, 2014
This is version 75 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