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P39045

- DAC_ACTSP

UniProt

P39045 - DAC_ACTSP

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Protein
D-alanyl-D-alanine carboxypeptidase
Gene
dac
Organism
Actinomadura sp. (strain R39)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

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 regulationi

Inhibited by benzylpenicillin, cephaloridine, ampicillin and cetiofur.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei98 – 981Acyl-ester intermediate
Active sitei101 – 1011Proton acceptor
Active sitei347 – 3471 By similarity
Binding sitei459 – 4591Substrate

GO - Molecular functioni

  1. serine-type D-Ala-D-Ala carboxypeptidase activity Source: UniProtKB-EC

GO - Biological processi

  1. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  2. regulation of cell shape Source: UniProtKB-KW
  3. response to antibiotic Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Carboxypeptidase, Hydrolase, Protease

Keywords - Biological processi

Antibiotic resistance, Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

SABIO-RKP39045.
UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS13.002.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
Penicillin-binding protein
Short name:
PBP
Gene namesi
Name:dac
OrganismiActinomadura sp. (strain R39)
Taxonomic identifieri72570 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptosporangineaeThermomonosporaceaeActinomadura

Subcellular locationi

GO - Cellular componenti

  1. extracellular region Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 49491 Publication
Add
BLAST
Chaini50 – 515466D-alanyl-D-alanine carboxypeptidase
PRO_0000027240Add
BLAST
Propeptidei516 – 53823Removed in mature form
PRO_0000308945Add
BLAST

Interactioni

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi51 – 6111
Helixi65 – 673
Beta strandi71 – 788
Turni79 – 813
Beta strandi84 – 896
Helixi97 – 993
Helixi100 – 11112
Beta strandi117 – 12610
Beta strandi132 – 1354
Beta strandi137 – 1415
Beta strandi145 – 1473
Helixi149 – 16113
Beta strandi165 – 1673
Beta strandi171 – 1744
Helixi189 – 1913
Helixi195 – 1973
Beta strandi205 – 2073
Turni208 – 2114
Beta strandi212 – 22110
Beta strandi230 – 2323
Helixi234 – 2363
Turni237 – 2393
Beta strandi240 – 2445
Beta strandi247 – 2493
Beta strandi258 – 2603
Beta strandi267 – 2759
Beta strandi281 – 2866
Helixi290 – 30415
Beta strandi313 – 3153
Beta strandi326 – 33510
Helixi336 – 34611
Helixi349 – 36416
Helixi369 – 38214
Beta strandi395 – 3973
Beta strandi403 – 4053
Helixi406 – 41712
Beta strandi418 – 4214
Helixi422 – 4287
Helixi437 – 4404
Helixi441 – 4433
Turni451 – 4555
Beta strandi457 – 4593
Beta strandi466 – 4738
Beta strandi480 – 4878
Beta strandi490 – 4923
Helixi495 – 50814

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP39045.
SMRiP39045. Positions 50-515.

Miscellaneous databases

EvolutionaryTraceiP39045.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni146 – 319174Absent in class-A beta-lactamases
Add
BLAST

Sequence similaritiesi

Belongs to the peptidase S13 family.

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.40.710.10. 2 hits.
InterProiIPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view]
PfamiPF02113. Peptidase_S13. 1 hit.
[Graphical view]
PRINTSiPR00922. DADACBPTASE3.
SUPFAMiSSF56601. SSF56601. 1 hit.
TIGRFAMsiTIGR00666. PBP4. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P39045-1 [UniParc]FASTAAdd to Basket

« Hide

MKQSSPEPLR PRRTGGRGGA RRAAALVTIP LLPMTLLGAS PALADASGAR    50
LTELREDIDA ILEDPALEGA VSGVVVVDTA TGEELYSRDG GEQLLPASNM 100
KLFTAAAALE VLGADHSFGT EVAAESAPGR RGEVQDLYLV GRGDPTLSAE 150
DLDAMAAEVA ASGVRTVRGD LYADDTWFDS ERLVDDWWPE DEPYAYSAQI 200
SALTVAHGER FDTGVTEVSV TPAAEGEPAD VDLGAAEGYA ELDNRAVTGA 250
AGSANTLVID RPVGTNTIAV TGSLPADAAP VTALRTVDEP AALAGHLFEE 300
ALESNGVTVK GDVGLGGVPA DWQDAEVLAD HTSAELSEIL VPFMKFSNNG 350
HAEMLVKSIG QETAGAGTWD AGLVGVEEAL SGLGVDTAGL VLNDGSGLSR 400
GNLVTADTVV DLLGQAGSAP WAQTWSASLP VAGESDPFVG GTLANRMRGT 450
AAEGVVEAKT GTMSGVSALS GYVPGPEGEL AFSIVNNGHS GPAPLAVQDA 500
IAVRLAEYAG HQAPEGARMM RGPVQGSGEL ECSWVQAC 538
Length:538
Mass (Da):54,974
Last modified:February 1, 1995 - v1
Checksum:i58A8300C32802E7B
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti100 – 1012MK → GV AA sequence 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X64790 Genomic DNA. Translation: CAA46023.1.
PIRiS22409.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X64790 Genomic DNA. Translation: CAA46023.1 .
PIRi S22409.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1W79 X-ray 1.80 A/B/C/D 50-538 [» ]
1W8Q X-ray 2.85 A/B/C/D 50-538 [» ]
1W8Y X-ray 2.40 A/B/C/D 50-538 [» ]
2VGJ X-ray 2.40 A/B/C/D 50-538 [» ]
2VGK X-ray 2.25 A/B/C/D 50-538 [» ]
2WKE X-ray 2.20 A/B/C/D 50-515 [» ]
2XDM X-ray 2.40 A/B/C/D 50-515 [» ]
2XK1 X-ray 2.80 A/B/C/D 50-515 [» ]
2XLN X-ray 2.40 A/B/C/D 50-538 [» ]
2Y4A X-ray 2.70 A/B/C/D 50-515 [» ]
2Y55 X-ray 2.60 A/B/C/D 50-515 [» ]
2Y59 X-ray 2.50 A/B/C/D 50-515 [» ]
3ZCZ X-ray 2.60 A/B/C/D 50-516 [» ]
3ZVT X-ray 3.10 A/B/C/D 50-515 [» ]
3ZVW X-ray 2.00 A/B/C/D 50-515 [» ]
4B4X X-ray 2.65 A/B/C/D 50-515 [» ]
4B4Z X-ray 2.20 A/B/C/D 50-515 [» ]
4BEN X-ray 2.15 A/B/C/D 50-515 [» ]
ProteinModelPortali P39045.
SMRi P39045. Positions 50-515.
ModBasei Search...
MobiDBi Search...

Chemistry

BindingDBi P39045.
ChEMBLi CHEMBL6016.

Protein family/group databases

MEROPSi S13.002.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00219 .
SABIO-RK P39045.

Miscellaneous databases

EvolutionaryTracei P39045.

Family and domain databases

Gene3Di 3.40.710.10. 2 hits.
InterProi IPR012338. Beta-lactam/transpept-like.
IPR000667. Peptidase_S13.
[Graphical view ]
Pfami PF02113. Peptidase_S13. 1 hit.
[Graphical view ]
PRINTSi PR00922. DADACBPTASE3.
SUPFAMi SSF56601. SSF56601. 1 hit.
TIGRFAMsi TIGR00666. PBP4. 1 hit.
ProtoNeti Search...

Publicationsi

  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. "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.
  3. "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.
  4. "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.

Entry informationi

Entry nameiDAC_ACTSP
AccessioniPrimary (citable) accession number: P39045
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 9, 2014
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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