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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Vesicomyosocius okutanii subsp. Calyptogena okutanii (strain HA)
Status
Reviewed-Annotation score: 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

Pathway: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.UniRule annotation
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi245 – 2451Magnesium or manganese 1UniRule annotation
Metal bindingi258 – 2581Magnesium or manganese 1UniRule annotation
Metal bindingi258 – 2581Magnesium or manganese 2UniRule annotation
Metal bindingi260 – 2601Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi124 – 17754ATPUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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

BioCyciCVES412965:GHZZ-700-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:COSY_0701
OrganismiVesicomyosocius okutanii subsp. Calyptogena okutanii (strain HA)
Taxonomic identifieri412965 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriasulfur-oxidizing symbionts
ProteomesiUP000000247 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 293293D-alanine--D-alanine ligasePRO_0000341193Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi412965.COSY_0701.

Structurei

3D structure databases

ProteinModelPortaliA5CW55.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini98 – 291194ATP-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.
OMAiPFLLEMN.
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]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A5CW55-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIAILMGGNS AERAISLKSG EAIYQTLNNQ NIDCFTFDWY GDNLSEFWQQ
60 70 80 90 100
EFDQVFIILH GRGGEDGYIQ KQLENRGICY TGSDSNASHN SMDKARTKII
110 120 130 140 150
WEQHSLTLAP SIIANIDQPI NPINFPLPWA VKPTLEGSSI GISKVDNQMQ
160 170 180 190 200
LNDALMLAWQ YAPYALIEQW IKGDEYTVAI LGDKALPVVR IITDQNFYDY
210 220 230 240 250
ESKYHSNKTQ YLCPCNLSLT QEKALQAIAL KAFFAINAKG WGRVDFIINQ
260 270 280 290
HNKPYLLEIN TVPGMTSHSL VPMAAKAIGI SFNKLVTSII NEI
Length:293
Mass (Da):32,900
Last modified:June 12, 2007 - v1
Checksum:i6A04807F17E5B3D8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009247 Genomic DNA. Translation: BAF61813.1.
RefSeqiWP_011930083.1. NC_009465.1.
YP_001219537.1. NC_009465.1.

Genome annotation databases

EnsemblBacteriaiBAF61813; BAF61813; COSY_0701.
KEGGivok:COSY_0701.
PATRICi32021265. VBICanVes128383_0706.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP009247 Genomic DNA. Translation: BAF61813.1.
RefSeqiWP_011930083.1. NC_009465.1.
YP_001219537.1. NC_009465.1.

3D structure databases

ProteinModelPortaliA5CW55.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi412965.COSY_0701.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAF61813; BAF61813; COSY_0701.
KEGGivok:COSY_0701.
PATRICi32021265. VBICanVes128383_0706.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciCVES412965:GHZZ-700-MONOMER.

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]
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Reduced genome of the thioautotrophic intracellular symbiont in a deep-sea clam, Calyptogena okutanii."
    Kuwahara H., Yoshida T., Takaki Y., Shimamura S., Nishi S., Harada M., Matsuyama K., Takishita K., Kawato M., Uematsu K., Fujiwara Y., Sato T., Kato C., Kitagawa M., Kato I., Maruyama T.
    Curr. Biol. 17:881-886(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HA.

Entry informationi

Entry nameiDDL_VESOH
AccessioniPrimary (citable) accession number: A5CW55
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: June 12, 2007
Last modified: April 1, 2015
This is version 61 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.