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P07862 (DDLB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 143. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

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

EC=6.3.2.4
Alternative name(s):
D-Ala-D-Ala ligase B
D-alanylalanine synthetase B
Gene names
Name:ddlB
Synonyms:ddl
Ordered Locus Names:b0092, JW0090
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length306 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Cell wall formation. 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

Subunit structure

Monomer.

Subcellular location

Cytoplasm 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

Initiator methionine11Removed HAMAP-Rule MF_00047
Chain2 – 306305D-alanine--D-alanine ligase B HAMAP-Rule MF_00047
PRO_0000177818

Regions

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

Sites

Active site151
Active site1501
Active site2811
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

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

Details...

Sequences

Sequence LengthMass (Da)Tools
P07862 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: F2D401C323A04471

FASTA30632,840
        10         20         30         40         50         60 
MTDKIAVLLG GTSAEREVSL NSGAAVLAGL REGGIDAYPV DPKEVDVTQL KSMGFQKVFI 

        70         80         90        100        110        120 
ALHGRGGEDG TLQGMLELMG LPYTGSGVMA SALSMDKLRS KLLWQGAGLP VAPWVALTRA 

       130        140        150        160        170        180 
EFEKGLSDKQ LAEISALGLP VIVKPSREGS SVGMSKVVAE NALQDALRLA FQHDEEVLIE 

       190        200        210        220        230        240 
KWLSGPEFTV AILGEEILPS IRIQPSGTFY DYEAKYLSDE TQYFCPAGLE ASQEANLQAL 

       250        260        270        280        290        300 
VLKAWTTLGC KGWGRIDVML DSDGQFYLLE ANTSPGMTSH SLVPMAARQA GMSFSQLVVR 


ILELAD 

« Hide

References

« Hide 'large scale' references
[1]"Further evidence for overlapping transcriptional units in an Escherichia coli cell envelope-cell division gene cluster: DNA sequence and transcriptional organization of the ddl ftsQ region."
Robinson A.C., Kenan D.J., Sweeney J., Donachie W.D.
J. Bacteriol. 167:809-817(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Nucleotide sequence involving murG and murC in the mra gene cluster region of Escherichia coli."
Ikeda M., Wachi M., Jung H.K., Ishino F., Matsuhashi M.
Nucleic Acids Res. 18:4014-4014(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-41.
Strain: K12.
[6]"Regulation of expression of the ftsA cell division gene by sequences in upstream genes."
Dewar S.J., Donachie W.D.
J. Bacteriol. 172:6611-6614(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 300-306.
[7]"D-alanine:D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme."
Al-Bar O.A., O'Connor C.D., Giles I.G., Akhtar M.
Biochem. J. 282:747-752(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION, PARTIAL PROTEIN SEQUENCE.
[8]"Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3-A resolution."
Fan C., Moews P.C., Walsh C.T., Knox J.R.
Science 266:439-443(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[9]"D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant."
Fan C., Park I.-S., Walsh C.T., Knox J.R.
Biochemistry 36:2531-2538(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M14029 Genomic DNA. Translation: AAA23672.1.
K02668 Genomic DNA. Translation: AAA23815.1.
X52644 Genomic DNA. Translation: CAA36869.1.
X55034 Genomic DNA. Translation: CAA38869.1.
U00096 Genomic DNA. Translation: AAC73203.1.
AP009048 Genomic DNA. Translation: BAB96660.1.
PIRCEECDL. A30289.
RefSeqNP_414634.1. NC_000913.3.
YP_488397.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1IOVX-ray2.20A1-306[»]
1IOWX-ray1.90A1-306[»]
2DLNX-ray2.30A1-306[»]
ProteinModelPortalP07862.
SMRP07862. Positions 1-306.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP07862. 1 interaction.
STRING511145.b0092.

Chemistry

ChEMBLCHEMBL1956.

Proteomic databases

PaxDbP07862.
PRIDEP07862.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73203; AAC73203; b0092.
BAB96660; BAB96660; BAB96660.
GeneID12932120.
946324.
KEGGecj:Y75_p0091.
eco:b0092.
PATRIC32115289. VBIEscCol129921_0096.

Organism-specific databases

EchoBASEEB0210.
EcoGeneEG10214. ddlB.

Phylogenomic databases

eggNOGCOG1181.
HOGENOMHOG000011592.
KOK01921.
OMADTQYRIP.
OrthoDBEOG6ND0KB.
ProtClustDBPRK01372.

Enzyme and pathway databases

BioCycEcoCyc:DALADALALIGB-MONOMER.
ECOL316407:JW0090-MONOMER.
MetaCyc:DALADALALIGB-MONOMER.
UniPathwayUPA00219.

Gene expression databases

GenevestigatorP07862.

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...

Other

EvolutionaryTraceP07862.
PROP07862.

Entry information

Entry nameDDLB_ECOLI
AccessionPrimary (citable) accession number: P07862
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 143 of the entry and version 3 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene