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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nitrosomonas europaea (strain ATCC 19718 / NBRC 14298)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi254 – 2541Magnesium or manganese 1UniRule annotation
Metal bindingi267 – 2671Magnesium or manganese 1UniRule annotation
Metal bindingi267 – 2671Magnesium or manganese 2UniRule annotation
Metal bindingi269 – 2691Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi131 – 18656ATPUniRule 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

BioCyciNEUR228410:GJNO-1017-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
Synonyms:ddlB
Ordered Locus Names:NE0994
OrganismiNitrosomonas europaea (strain ATCC 19718 / NBRC 14298)
Taxonomic identifieri228410 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNitrosomonadalesNitrosomonadaceaeNitrosomonas
ProteomesiUP000001416: Chromosome

Subcellular locationi

Cytoplasm 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 – 305305D-alanine--D-alanine ligasePRO_0000177847Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi228410.NE0994.

Structurei

3D structure databases

ProteinModelPortaliQ82VS0.
SMRiQ82VS0. Positions 7-302.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini105 – 300196ATP-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.
PhylomeDBiQ82VS0.

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.

Q82VS0-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNTRDVGKVA VLLGGRSAER EISLRSGQAV LAALQRSRVN AHAFDPAGQP
60 70 80 90 100
LENLLQQGFD RVFIALHGRY GEDGSVQGAL ELMELPYTGS GILASALAMD
110 120 130 140 150
KWRTKMIWQA AGINTPDYVM LDASSRFRDV ADRLGLPLII KPAREGSTLG
160 170 180 190 200
LNKVDNEQDF RSAYQAAAEY DSLVLAEQFI QGIELTAAIL DDMPLPLVRI
210 220 230 240 250
DVAEGLYDYQ AKYFSESTRY TCPSGLSAAL TTRIQEQALY AHRILGCTGW
260 270 280 290 300
SRVDLILDEN EQPFFLETNT SPGMTDHSLV PMAAKAAGIS FDELVVQILE

LSCEH
Length:305
Mass (Da):33,442
Last modified:June 1, 2003 - v1
Checksum:i54B1F11950432305
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL954747 Genomic DNA. Translation: CAD84905.1.
RefSeqiNP_841067.1. NC_004757.1.
WP_011111603.1. NC_004757.1.

Genome annotation databases

EnsemblBacteriaiCAD84905; CAD84905; NE0994.
GeneIDi1081936.
KEGGineu:NE0994.
PATRICi22713008. VBINitEur56163_1105.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL954747 Genomic DNA. Translation: CAD84905.1.
RefSeqiNP_841067.1. NC_004757.1.
WP_011111603.1. NC_004757.1.

3D structure databases

ProteinModelPortaliQ82VS0.
SMRiQ82VS0. Positions 7-302.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi228410.NE0994.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAD84905; CAD84905; NE0994.
GeneIDi1081936.
KEGGineu:NE0994.
PATRICi22713008. VBINitEur56163_1105.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiPFLLEMN.
OrthoDBiEOG6ND0KB.
PhylomeDBiQ82VS0.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciNEUR228410:GJNO-1017-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]
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]
ProtoNetiSearch...

Publicationsi

  1. "Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea."
    Chain P., Lamerdin J.E., Larimer F.W., Regala W., Lao V., Land M.L., Hauser L., Hooper A.B., Klotz M.G., Norton J., Sayavedra-Soto L.A., Arciero D.M., Hommes N.G., Whittaker M.M., Arp D.J.
    J. Bacteriol. 185:2759-2773(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19718 / NBRC 14298.

Entry informationi

Entry nameiDDL_NITEU
AccessioniPrimary (citable) accession number: Q82VS0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 2003
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 82 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

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.