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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
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

Pathwayi: 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)DescriptionActionsGraphical viewLength
Metal bindingi259Magnesium or manganese 1UniRule annotation1
Metal bindingi272Magnesium or manganese 1UniRule annotation1
Metal bindingi272Magnesium or manganese 2UniRule annotation1
Metal bindingi274Magnesium or manganese 2UniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi136 – 191ATPUniRule annotationAdd BLAST56

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLigase
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
LigandATP-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:MCA2426
OrganismiMethylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
Taxonomic identifieri243233 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaMethylococcalesMethylococcaceaeMethylococcus
Proteomesi
  • UP000006821 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003411341 – 309D-alanine--D-alanine ligaseAdd BLAST309

Interactioni

Protein-protein interaction databases

STRINGi243233.MCA2426.

Structurei

3D structure databases

ProteinModelPortaliQ604W0.
SMRiQ604W0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini110 – 305ATP-graspUniRule annotationAdd BLAST196

Sequence similaritiesi

Belongs to the D-alanine--D-alanine ligase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CPF. Bacteria.
COG1181. LUCA.
HOGENOMiHOG000011592.
KOiK01921.
OMAiMQGLLEC.
OrthoDBiPOG091H00GT.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
HAMAPiMF_00047. Dala_Dala_lig. 1 hit.
InterProiView protein in InterPro
IPR011761. ATP-grasp.
IPR013815. ATP_grasp_subdomain_1.
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.
PfamiView protein in Pfam
PF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 1 hit.
PIRSFiPIRSF039102. Ddl/VanB. 1 hit.
SUPFAMiSSF52440. SSF52440. 1 hit.
TIGRFAMsiTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEiView protein in PROSITE
PS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.

Sequencei

Sequence statusi: Complete.

Q604W0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKRIQQASK FGKVAVLMGG SAAEREISLK SGKAVLEALR SGGIDAEGID
60 70 80 90 100
VGRDLIAPLL ERRFDRVFNV IHGRGGEDGV LQGALACLRV PCTGSGVLAS
110 120 130 140 150
ALSMDKLRTK LCWTGAGLPT PPWLRLDSPD DLERCRQALG FPVIVKPAEE
160 170 180 190 200
GSSIGMSRAA TAEELAQAWE RASGYGCAVF AERWIDGVEY TGGMLKGVPL
210 220 230 240 250
PLIRLETPHA FYDFDAKYRA DTTRYHCPCG LDTGREAELQ ALVLRACQIV
260 270 280 290 300
GVSGWGRVDL LVDRSGQPWL IEVNTVPGMT DHSLVPMAAK AAGIDFQELV

WHILETSFA
Length:309
Mass (Da):33,377
Last modified:November 23, 2004 - v1
Checksum:iF853B8EEE4568BE4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017282 Genomic DNA. Translation: AAU91482.1.

Genome annotation databases

EnsemblBacteriaiAAU91482; AAU91482; MCA2426.
KEGGimca:MCA2426.

Similar proteinsi

Entry informationi

Entry nameiDDL_METCA
AccessioniPrimary (citable) accession number: Q604W0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: November 23, 2004
Last modified: August 30, 2017
This is version 93 of the entry and version 1 of the sequence. See 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