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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 – 3471By similarity
Binding sitei459 – 4591Substrate

GO - Molecular functioni

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

GO - Biological processi

  1. cell wall organization Source: UniProtKB-KW
  2. peptidoglycan biosynthetic process Source: UniProtKB-UniPathway
  3. regulation of cell shape Source: UniProtKB-KW
  4. 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-KW
Complete GO annotation...

Keywords - Cellular componenti

Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 49491 PublicationAdd
BLAST
Chaini50 – 515466D-alanyl-D-alanine carboxypeptidasePRO_0000027240Add
BLAST
Propeptidei516 – 53823Removed in mature formPRO_0000308945Add
BLAST

Interactioni

Structurei

Secondary structure

1
538
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi51 – 6111Combined sources
Helixi65 – 673Combined sources
Beta strandi71 – 788Combined sources
Turni79 – 813Combined sources
Beta strandi84 – 896Combined sources
Helixi97 – 993Combined sources
Helixi100 – 11112Combined sources
Beta strandi117 – 12610Combined sources
Beta strandi132 – 1354Combined sources
Beta strandi137 – 1415Combined sources
Beta strandi145 – 1473Combined sources
Helixi149 – 16113Combined sources
Beta strandi165 – 1673Combined sources
Beta strandi171 – 1744Combined sources
Helixi189 – 1913Combined sources
Helixi195 – 1973Combined sources
Beta strandi205 – 2073Combined sources
Turni208 – 2114Combined sources
Beta strandi212 – 22110Combined sources
Beta strandi230 – 2323Combined sources
Helixi234 – 2363Combined sources
Turni237 – 2393Combined sources
Beta strandi240 – 2445Combined sources
Beta strandi247 – 2493Combined sources
Beta strandi258 – 2603Combined sources
Beta strandi267 – 2759Combined sources
Beta strandi281 – 2866Combined sources
Helixi290 – 30415Combined sources
Beta strandi313 – 3153Combined sources
Beta strandi326 – 33510Combined sources
Helixi336 – 34611Combined sources
Helixi349 – 36416Combined sources
Helixi369 – 38214Combined sources
Beta strandi395 – 3973Combined sources
Beta strandi403 – 4053Combined sources
Helixi406 – 41712Combined sources
Beta strandi418 – 4214Combined sources
Helixi422 – 4287Combined sources
Helixi437 – 4404Combined sources
Helixi441 – 4433Combined sources
Turni451 – 4555Combined sources
Beta strandi457 – 4593Combined sources
Beta strandi466 – 4738Combined sources
Beta strandi480 – 4878Combined sources
Beta strandi490 – 4923Combined sources
Helixi495 – 50814Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39045.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the peptidase S13 family.Curated

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

        10         20         30         40         50
MKQSSPEPLR PRRTGGRGGA RRAAALVTIP LLPMTLLGAS PALADASGAR
60 70 80 90 100
LTELREDIDA ILEDPALEGA VSGVVVVDTA TGEELYSRDG GEQLLPASNM
110 120 130 140 150
KLFTAAAALE VLGADHSFGT EVAAESAPGR RGEVQDLYLV GRGDPTLSAE
160 170 180 190 200
DLDAMAAEVA ASGVRTVRGD LYADDTWFDS ERLVDDWWPE DEPYAYSAQI
210 220 230 240 250
SALTVAHGER FDTGVTEVSV TPAAEGEPAD VDLGAAEGYA ELDNRAVTGA
260 270 280 290 300
AGSANTLVID RPVGTNTIAV TGSLPADAAP VTALRTVDEP AALAGHLFEE
310 320 330 340 350
ALESNGVTVK GDVGLGGVPA DWQDAEVLAD HTSAELSEIL VPFMKFSNNG
360 370 380 390 400
HAEMLVKSIG QETAGAGTWD AGLVGVEEAL SGLGVDTAGL VLNDGSGLSR
410 420 430 440 450
GNLVTADTVV DLLGQAGSAP WAQTWSASLP VAGESDPFVG GTLANRMRGT
460 470 480 490 500
AAEGVVEAKT GTMSGVSALS GYVPGPEGEL AFSIVNNGHS GPAPLAVQDA
510 520 530
IAVRLAEYAG HQAPEGARMM RGPVQGSGEL ECSWVQAC
Length:538
Mass (Da):54,974
Last modified:February 1, 1995 - v1
Checksum:i58A8300C32802E7B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti100 – 1012MK → GV AA sequence (PubMed:7305936)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X64790 Genomic DNA. Translation: CAA46023.1.
PIRiS22409.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X64790 Genomic DNA. Translation: CAA46023.1 .
PIRi S22409.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 90 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