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Protein

D-alanine--D-alanine ligase

Gene

ddl

Organism
Nitrosomonas eutropha (strain C91)
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:ipeptidoglycan 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 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

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

BioCyciNEUT335283:GHT6-252-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:Neut_0243
OrganismiNitrosomonas eutropha (strain C91)
Taxonomic identifieri335283 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNitrosomonadalesNitrosomonadaceaeNitrosomonas
ProteomesiUP000001966 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 – 306306D-alanine--D-alanine ligasePRO_1000030474Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi335283.Neut_0243.

Structurei

3D structure databases

ProteinModelPortaliQ0AJE4.
SMRiQ0AJE4. 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.
OMAiYLCPCGL.
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.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q0AJE4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIRDLGKVA VLLGGRSAER EISLKSGHAV LAALQRSQVD AHAFDPVGQP
60 70 80 90 100
LEDLLKQGFD RAFIALHGRY GEDGSVQGAL ELMDLPYTGS GILASALAMD
110 120 130 140 150
KWRTKMIWQA AGISTPDYVM LDADSNFQEV TDRLGLPLII KPAREGSTIG
160 170 180 190 200
LNKVDYAQDM QSAYQTAAQH DSLVIAEQFI QGIELTAAIL DDVPLPLVRI
210 220 230 240 250
DVTEGLYDYQ AKYFSESTRY TCPSGLSKIL TTRIQEQALY AHRILGCTGW
260 270 280 290 300
SRVDLILDKN GQPFFLEANT SPGMTNHSLV PMAAQAAGIS FDELVIQILE

LSCEYA
Length:306
Mass (Da):33,438
Last modified:October 17, 2006 - v1
Checksum:iD9694CD436BB26A4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000450 Genomic DNA. Translation: ABI58527.1.
RefSeqiWP_011633371.1. NC_008344.1.

Genome annotation databases

EnsemblBacteriaiABI58527; ABI58527; Neut_0243.
KEGGinet:Neut_0243.
PATRICi22717436. VBINitEut7577_0396.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000450 Genomic DNA. Translation: ABI58527.1.
RefSeqiWP_011633371.1. NC_008344.1.

3D structure databases

ProteinModelPortaliQ0AJE4.
SMRiQ0AJE4. Positions 7-302.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi335283.Neut_0243.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABI58527; ABI58527; Neut_0243.
KEGGinet:Neut_0243.
PATRICi22717436. VBINitEut7577_0396.

Phylogenomic databases

eggNOGiCOG1181.
HOGENOMiHOG000011592.
KOiK01921.
OMAiYLCPCGL.
OrthoDBiEOG6ND0KB.

Enzyme and pathway databases

UniPathwayiUPA00219.
BioCyciNEUT335283:GHT6-252-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.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation."
    Stein L.Y., Arp D.J., Berube P.M., Chain P.S., Hauser L., Jetten M.S., Klotz M.G., Larimer F.W., Norton J.M., Op den Camp H.J.M., Shin M., Wei X.
    Environ. Microbiol. 9:2993-3007(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C91.

Entry informationi

Entry nameiDDL_NITEC
AccessioniPrimary (citable) accession number: Q0AJE4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 17, 2006
Last modified: July 22, 2015
This is version 69 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.