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Q3J792 (DDL_NITOC) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 65. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
D-alanine--D-alanine ligase

EC=6.3.2.4
Alternative name(s):
D-Ala-D-Ala ligase
D-alanylalanine synthetase
Gene names
Name:ddl
Ordered Locus Names:Noc_2858
OrganismNitrosococcus oceani (strain ATCC 19707 / NCIMB 11848) [Complete proteome] [HAMAP]
Taxonomic identifier323261 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaChromatialesChromatiaceaeNitrosococcus

Protein attributes

Sequence length316 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Cell wall formation By similarity. HAMAP-Rule MF_00047

Catalytic activity

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. HAMAP-Rule MF_00047

Cofactor

Binds 2 magnesium or manganese ions per subunit By similarity.

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis. HAMAP-Rule MF_00047

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00047.

Sequence similarities

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

Contains 1 ATP-grasp domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 316316D-alanine--D-alanine ligase HAMAP-Rule MF_00047
PRO_0000341138

Regions

Domain109 – 304196ATP-grasp
Nucleotide binding135 – 19056ATP By similarity

Sites

Metal binding2581Magnesium or manganese 1 By similarity
Metal binding2711Magnesium or manganese 1 By similarity
Metal binding2711Magnesium or manganese 2 By similarity
Metal binding2731Magnesium or manganese 2 By similarity

Sequences

Sequence LengthMass (Da)Tools
Q3J792 [UniParc].

Last modified November 8, 2005. Version 1.
Checksum: 24A361ED8DBEF4CF

FASTA31634,489
        10         20         30         40         50         60 
MIGRVDVKAW GKVVVLMGGY SAEREISLKS GTAVLQSLLR QGIEAHGIDV DKGVLTQLSK 

        70         80         90        100        110        120 
GQFTRAFIAL HGRGGEDGVI QGVLETLNLP YTGSGVLGSA LTMDKLRSKR LWRGMDLPTA 

       130        140        150        160        170        180 
DFSVLTRDTN PALIAADLGL PLIVKPAREG SSLGMMKVES IEALQSAYRE AVIFDTAVFA 

       190        200        210        220        230        240 
ERWLPGAEYT AAILADRVLP LIRLETPRVF YDFEAKYHAN TTRYFCPCGL SEKQEQDLQA 

       250        260        270        280        290        300 
LALEAFQALG ASGWGRVDLR CDEKAHPYLL EINTVPGMTD HSLVPMAAQA AGIEFDEMVL 

       310 
QILASSLERR MFQDGT 

« Hide

References

[1]"Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707."
Klotz M.G., Arp D.J., Chain P.S.G., El-Sheikh A.F., Hauser L.J., Hommes N.G., Larimer F.W., Malfatti S.A., Norton J.M., Poret-Peterson A.T., Vergez L.M., Ward B.B.
Appl. Environ. Microbiol. 72:6299-6315(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 19707 / NCIMB 11848.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000127 Genomic DNA. Translation: ABA59304.1.
RefSeqYP_344834.1. NC_007484.1.

3D structure databases

ProteinModelPortalQ3J792.
SMRQ3J792. Positions 11-304.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING323261.Noc_2858.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABA59304; ABA59304; Noc_2858.
GeneID3705399.
KEGGnoc:Noc_2858.
PATRIC22710224. VBINitOce57959_3312.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG1181.
HOGENOMHOG000011592.
KOK01921.
OMAANDTQYR.
OrthoDBEOG6ND0KB.

Enzyme and pathway databases

BioCycNOCE323261:GCI3-2907-MONOMER.
UniPathwayUPA00219.

Family and domain databases

Gene3D3.30.1490.20. 1 hit.
3.30.470.20. 2 hits.
3.40.50.20. 1 hit.
HAMAPMF_00047. Dala_Dala_lig.
InterProIPR011761. 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]
PANTHERPTHR23132. PTHR23132. 1 hit.
PfamPF07478. Dala_Dala_lig_C. 1 hit.
PF01820. Dala_Dala_lig_N. 2 hits.
[Graphical view]
SUPFAMSSF52440. SSF52440. 1 hit.
TIGRFAMsTIGR01205. D_ala_D_alaTIGR. 1 hit.
PROSITEPS50975. ATP_GRASP. 1 hit.
PS00843. DALA_DALA_LIGASE_1. 1 hit.
PS00844. DALA_DALA_LIGASE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDDL_NITOC
AccessionPrimary (citable) accession number: Q3J792
Entry history
Integrated into UniProtKB/Swiss-Prot: June 10, 2008
Last sequence update: November 8, 2005
Last modified: May 14, 2014
This is version 65 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PATHWAY comments

Index of metabolic and biosynthesis pathways