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D3PM04 (D3PM04_MEIRD) Unreviewed, UniProtKB/TrEMBL

Last modified February 19, 2014. Version 34. Feed History...

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

Protein namesRecommended name:
D-alanine--D-alanine ligase HAMAP-Rule MF_00047

EC=6.3.2.4 HAMAP-Rule MF_00047
Alternative name(s):
D-Ala-D-Ala ligase HAMAP-Rule MF_00047
D-alanylalanine synthetase HAMAP-Rule MF_00047
Gene names
Name:ddl HAMAP-Rule MF_00047 EMBL AGK03569.1
Ordered Locus Names:Mrub_0337 EMBL ADD27115.1
ORF Names:K649_01305 EMBL AGK03569.1
OrganismMeiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21) (Thermus ruber) [Complete proteome] [HAMAP] EMBL ADD27115.1
Taxonomic identifier504728 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeMeiothermus

Protein attributes

Sequence length322 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Cell wall formation By similarity. SAAS SAAS005905 HAMAP-Rule MF_00047

Catalytic activity

ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine. SAAS SAAS005905 HAMAP-Rule MF_00047

Cofactor

Binds 2 magnesium or manganese ions per subunit By similarity. SAAS SAAS005905 HAMAP-Rule MF_00047

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis. SAAS SAAS005905 HAMAP-Rule MF_00047

Subcellular location

Cytoplasm By similarity SAAS SAAS005905 HAMAP-Rule MF_00047.

Sequence similarities

Belongs to the D-alanine--D-alanine ligase family. HAMAP-Rule MF_00047

Contains 1 ATP-grasp domain. HAMAP-Rule MF_00047

Contains ATP-grasp domain. SAAS SAAS005905

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Domain120 – 317198ATP-grasp By similarity HAMAP-Rule MF_00047
Nucleotide binding146 – 19954ATP By similarity HAMAP-Rule MF_00047

Sites

Metal binding2711Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047
Metal binding2841Magnesium or manganese 1 By similarity HAMAP-Rule MF_00047
Metal binding2841Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047
Metal binding2861Magnesium or manganese 2 By similarity HAMAP-Rule MF_00047

Sequences

Sequence LengthMass (Da)Tools
D3PM04 [UniParc].

Last modified April 20, 2010. Version 1.
Checksum: 396C70BD2892732B

FASTA32235,231
        10         20         30         40         50         60 
MKVLLLAGGP PGEHEVSLSS ARGVLAAMPH PTELVVIAKD GRWLLGEDAY EALRAGVAEQ 

        70         80         90        100        110        120 
GTHPFPPPVP WQHYDVVFPL LHGPLGEDGV IQGFLQLLRR PYVGAGVASS ALCMDKDLCK 

       130        140        150        160        170        180 
RVLRQAGIPV VPWVTLYKGE PTPQPPFPPP YFVKPANTGS SVGISKVKAD QDATRALAEA 

       190        200        210        220        230        240 
FAWDDKVLVE QGIEGVRELE VALLGNIHAE ASVVGEITYQ SEFYDYETKY TEGKAQLHLP 

       250        260        270        280        290        300 
APIPPELSDE IRATALEAYR ILGVRGMARV DFFLSPQGEL YLNEFNTIPG FTPTSMYPKL 

       310        320 
WQATGLAYPD LLDRLVRLAL ER 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of Meiothermus ruber type strain (21)."
Tindall B.J., Sikorski J., Lucas S., Goltsman E., Copeland A., Glavina Del Rio T., Nolan M., Tice H., Cheng J.F., Han C., Pitluck S., Liolios K., Ivanova N., Mavromatis K., Ovchinnikova G., Pati A., Fahnrich R., Goodwin L. expand/collapse author list , Chen A., Palaniappan K., Land M., Hauser L., Chang Y.J., Jeffries C.D., Rohde M., Goker M., Woyke T., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.P., Lapidus A.
Stand. Genomic Sci. 3:26-36(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 35948 / DSM 1279 / VKM B-1258 / 21.
[2]"Non-Hybrid, Finished Microbial Genome Assemblies from Long-Read SMRT Sequencing Data."
Klammer A., Drake J., Heiner C., Clum A., Copeland A., Huddleston J., Eichler E., Turner S.W.
Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: DSM 1279 EMBL AGK03569.1.
[3]Chin J., Alexander D.H., Marks P., Korlach J., Clum A., Copeland A.
Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: DSM 1279 EMBL AGK03569.1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001743 Genomic DNA. Translation: ADD27115.1.
CP005385 Genomic DNA. Translation: AGK03569.1.
RefSeqYP_003506135.1. NC_013946.1.
YP_007879066.1. NC_021081.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaADD27115; ADD27115; Mrub_0337.
AGK03569; AGK03569; K649_01305.
GeneID15334879.
8878408.
KEGGmrb:Mrub_0337.
mre:K649_01305.
PATRIC35356778. VBIMeiRub128672_0343.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000011593.
KOK01921.
OMAMDKIAMK.

Enzyme and pathway databases

BioCycMRUB504728:GI6U-342-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. 1 hit.
[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.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameD3PM04_MEIRD
AccessionPrimary (citable) accession number: D3PM04
Entry history
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: February 19, 2014
This is version 34 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)