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P39045 (DAC_ACTSP) Reviewed, UniProtKB/Swiss-Prot

Last modified December 11, 2013. Version 85. 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-alanyl-D-alanine carboxypeptidase

Short name=DD-carboxypeptidase
Short name=DD-peptidase
EC=3.4.16.4
Alternative name(s):
Penicillin-binding protein
Short name=PBP
Gene names
Name:dac
OrganismActinomadura sp. (strain R39)
Taxonomic identifier72570 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptosporangineaeThermomonosporaceaeActinomadura

Protein attributes

Sequence length538 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.

Catalytic activity

Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.

Enzyme regulation

Inhibited by benzylpenicillin, cephaloridine, ampicillin and cetiofur. Ref.4

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis.

Subcellular location

Secreted.

Sequence similarities

Belongs to the peptidase S13 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 4949 Ref.1
Chain50 – 515466D-alanyl-D-alanine carboxypeptidase
PRO_0000027240
Propeptide516 – 53823Removed in mature form
PRO_0000308945

Regions

Region146 – 319174Absent in class-A beta-lactamases

Sites

Active site981Acyl-ester intermediate
Active site1011Proton acceptor
Active site3471 By similarity
Binding site4591Substrate

Experimental info

Sequence conflict100 – 1012MK → GV AA sequence Ref.3

Secondary structure

.................................................................................. 538
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P39045 [UniParc].

Last modified February 1, 1995. Version 1.
Checksum: 58A8300C32802E7B

FASTA53854,974
        10         20         30         40         50         60 
MKQSSPEPLR PRRTGGRGGA RRAAALVTIP LLPMTLLGAS PALADASGAR LTELREDIDA 

        70         80         90        100        110        120 
ILEDPALEGA VSGVVVVDTA TGEELYSRDG GEQLLPASNM KLFTAAAALE VLGADHSFGT 

       130        140        150        160        170        180 
EVAAESAPGR RGEVQDLYLV GRGDPTLSAE DLDAMAAEVA ASGVRTVRGD LYADDTWFDS 

       190        200        210        220        230        240 
ERLVDDWWPE DEPYAYSAQI SALTVAHGER FDTGVTEVSV TPAAEGEPAD VDLGAAEGYA 

       250        260        270        280        290        300 
ELDNRAVTGA AGSANTLVID RPVGTNTIAV TGSLPADAAP VTALRTVDEP AALAGHLFEE 

       310        320        330        340        350        360 
ALESNGVTVK GDVGLGGVPA DWQDAEVLAD HTSAELSEIL VPFMKFSNNG HAEMLVKSIG 

       370        380        390        400        410        420 
QETAGAGTWD AGLVGVEEAL SGLGVDTAGL VLNDGSGLSR GNLVTADTVV DLLGQAGSAP 

       430        440        450        460        470        480 
WAQTWSASLP VAGESDPFVG GTLANRMRGT AAEGVVEAKT GTMSGVSALS GYVPGPEGEL 

       490        500        510        520        530 
AFSIVNNGHS GPAPLAVQDA IAVRLAEYAG HQAPEGARMM RGPVQGSGEL ECSWVQAC 

« Hide

References

[1]"Primary and predicted secondary structures of the Actinomadura R39 extracellular DD-peptidase, a penicillin-binding protein (PBP) related to the Escherichia coli PBP4."
Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O., van Beeumen J., Frere J.-M., Ghuysen J.-M.
Biochem. J. 282:781-788(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 50-87.
[2]Erratum
Granier B., Duez C., Lepage S., Englebert S., Dusart J., Dideberg O., van Beeumen J., Frere J.-M., Ghuysen J.-M.
Biochem. J. 286:981-982(1992) [PubMed] [Europe PMC] [Abstract]
[3]"The penicillin-binding site in the exocellular DD-carboxypeptidase-transpeptidase of Actinomadura R39."
Duez C., Joris B., Frere J.-M., Ghuysen J.-M., van Beeumen J.
Biochem. J. 193:83-86(1981) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 95-101, SUBSTRATE-BINDING SITE.
[4]"Purification and characterization of PBP4a, a new low-molecular-weight penicillin-binding protein from Bacillus subtilis."
Duez C., Vanhove M., Gallet X., Bouillenne F., Docquier J.-D., Brans A., Frere J.-M.
J. Bacteriol. 183:1595-1599(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[5]"Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins."
Sauvage E., Herman R., Petrella S., Duez C., Bouillenne F., Frere J.-M., Charlier P.
J. Biol. Chem. 280:31249-31256(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 50-515 OF APOENZYME AND COMPLEX WITH NITROCEFIN, PROCESSING OF C-TERMINUS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X64790 Genomic DNA. Translation: CAA46023.1.
PIRS22409.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1W79X-ray1.80A/B/C/D50-538[»]
1W8QX-ray2.85A/B/C/D50-538[»]
1W8YX-ray2.40A/B/C/D50-538[»]
2VGJX-ray2.40A/B/C/D50-538[»]
2VGKX-ray2.25A/B/C/D50-538[»]
2WKEX-ray2.20A/B/C/D50-515[»]
2XDMX-ray2.40A/B/C/D50-515[»]
2XK1X-ray2.80A/B/C/D50-515[»]
2XLNX-ray2.40A/B/C/D50-538[»]
2Y4AX-ray2.70A/B/C/D50-515[»]
2Y55X-ray2.60A/B/C/D50-515[»]
2Y59X-ray2.50A/B/C/D50-515[»]
3ZCZX-ray2.60A/B/C/D50-516[»]
3ZVTX-ray3.10A/B/C/D50-515[»]
3ZVWX-ray2.00A/B/C/D50-515[»]
4B4XX-ray2.65A/B/C/D50-515[»]
4B4ZX-ray2.20A/B/C/D50-515[»]
4BENX-ray2.15A/B/C/D50-515[»]
ProteinModelPortalP39045.
SMRP39045. Positions 50-515.
ModBaseSearch...
MobiDBSearch...

Chemistry

BindingDBP39045.
ChEMBLCHEMBL6016.

Protein family/group databases

MEROPSS13.002.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayUPA00219.

Family and domain databases

Gene3D3.40.710.10. 2 hits.
InterProIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSPR00922. DADACBPTASE3.
SUPFAMSSF56601. SSF56601. 1 hit.
TIGRFAMsTIGR00666. PBP4. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP39045.

Entry information

Entry nameDAC_ACTSP
AccessionPrimary (citable) accession number: P39045
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: December 11, 2013
This is version 85 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

Peptidase families

Classification of peptidase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways