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Q8ZIE7 (DDL_YERPE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 95. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | 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
Synonyms:ddlB
Ordered Locus Names:YPO0557, y3624, YP_3627
OrganismYersinia pestis [Reference proteome] [HAMAP]
Taxonomic identifier632 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Yersinia

Protein attributes

Sequence length306 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Cell wall formation By similarity.

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.

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 – 306306D-alanine--D-alanine ligase HAMAP-Rule MF_00047
PRO_0000177912

Regions

Domain101 – 303203ATP-grasp
Nucleotide binding134 – 18956ATP By similarity

Sites

Metal binding2571Magnesium or manganese 1 By similarity
Metal binding2701Magnesium or manganese 1 By similarity
Metal binding2701Magnesium or manganese 2 By similarity
Metal binding2721Magnesium or manganese 2 By similarity

Secondary structure

1 ........................................................ 306
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q8ZIE7 [UniParc].

Last modified March 1, 2002. Version 1.
Checksum: C78CFF3D2E11F846

FASTA30633,150
        10         20         30         40         50         60 
MAEKVAVLLG GTSAEREVSL LSGQAVLAGL KEAGIDAYGV DTKDFPVTQL KEQGFDKVFI 

        70         80         90        100        110        120 
ALHGRGGEDG TLQGVLEFLQ LPYTGSGVMA SALTMDKLRT KLVWQALGLP ISPYVALNRQ 

       130        140        150        160        170        180 
QFETLSPEEL VACVAKLGLP LIVKPSHEGS SVGMSKVDHA SELQKALVEA FQHDSDVLIE 

       190        200        210        220        230        240 
KWLSGPEFTV AILGDEVLPS IRIQPPGVFY DYDAKYLSDK TQYFCPSGLS DESEQQLAAL 

       250        260        270        280        290        300 
ALQAYHALDC SGWGRVDVMQ DRDGHFYLLE VNTSPGMTSH SLVPMAARQY GLSFSQLVAR 


ILMLAD

« Hide

References

[1]"Genome sequence of Yersinia pestis, the causative agent of plague."
Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G., Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L., Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M., Chillingworth T., Cronin A., Davies R.M. expand/collapse author list , Davis P., Dougan G., Feltwell T., Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S., Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J., Stevens K., Whitehead S., Barrell B.G.
Nature 413:523-527(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CO-92 / Biovar Orientalis.
[2]"Genome sequence of Yersinia pestis KIM."
Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P., Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D., Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A., Nilles M.L. expand/collapse author list , Matson J.S., Blattner F.R., Perry R.D.
J. Bacteriol. 184:4601-4611(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: KIM10+ / Biovar Mediaevalis.
[3]"Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans."
Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D., Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L., Dai R. expand/collapse author list , Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H., Wang J., Huang P., Yang R.
DNA Res. 11:179-197(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 91001 / Biovar Mediaevalis.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AL590842 Genomic DNA. Translation: CAL19236.1.
AE009952 Genomic DNA. Translation: AAM87172.1.
AE017042 Genomic DNA. Translation: AAS63775.1.
PIRAB0069.
RefSeqNP_670921.1. NC_004088.1.
NP_994898.1. NC_005810.1.
YP_002345628.1. NC_003143.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3V4ZX-ray2.69A/B1-306[»]
ProteinModelPortalQ8ZIE7.
SMRQ8ZIE7. Positions 1-306.
ModBaseSearch...

Protein-protein interaction databases

IntActQ8ZIE7. 3 interactions.
STRING214092.YPO0557.

Proteomic databases

PRIDEQ8ZIE7.

Protocols and materials databases

DNASU1148571.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAM87172; AAM87172; y3624.
AAS63775; AAS63775; YP_3627.
GeneID1148571.
1173401.
2763379.
KEGGype:YPO0557.
ypk:y3624.
ypm:YP_3627.

Phylogenomic databases

eggNOGCOG1181.
HOGENOMHOG000011592.
KOK01921.
OMAEVLVEKW.
ProtClustDBPRK01372.

Enzyme and pathway databases

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. PreATP-grasp-like. 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_YERPE
AccessionPrimary (citable) accession number: Q8ZIE7
Secondary accession number(s): Q0WJB0
Entry history
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: March 1, 2002
Last modified: May 1, 2013
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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