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Protein

D-alanyl-D-alanine carboxypeptidase

Gene

dac

Organism
Actinomadura sp. (strain R39)
Status
Reviewed-Annotation score: 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: peptidoglycan biosynthesis

This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.
View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei98Acyl-ester intermediate1
Active sitei101Proton acceptor1
Active sitei347By similarity1
Binding sitei459Substrate1

GO - Molecular functioni

GO - Biological processi

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

BRENDAi3.4.16.4. 9774.
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 lineageiBacteriaActinobacteriaStreptosporangialesThermomonosporaceaeActinomadura

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL6016.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 491 PublicationAdd BLAST49
ChainiPRO_000002724050 – 515D-alanyl-D-alanine carboxypeptidaseAdd BLAST466
PropeptideiPRO_0000308945516 – 538Removed in mature formAdd BLAST23

Interactioni

Chemistry databases

BindingDBiP39045.

Structurei

Secondary structure

1538
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi51 – 61Combined sources11
Helixi65 – 67Combined sources3
Beta strandi71 – 78Combined sources8
Turni79 – 81Combined sources3
Beta strandi84 – 89Combined sources6
Helixi97 – 99Combined sources3
Helixi100 – 111Combined sources12
Beta strandi117 – 126Combined sources10
Beta strandi132 – 135Combined sources4
Beta strandi137 – 141Combined sources5
Beta strandi145 – 147Combined sources3
Helixi149 – 161Combined sources13
Beta strandi165 – 167Combined sources3
Beta strandi171 – 174Combined sources4
Helixi189 – 191Combined sources3
Helixi195 – 197Combined sources3
Beta strandi205 – 207Combined sources3
Turni208 – 211Combined sources4
Beta strandi212 – 221Combined sources10
Beta strandi230 – 232Combined sources3
Helixi234 – 236Combined sources3
Turni237 – 239Combined sources3
Beta strandi240 – 244Combined sources5
Beta strandi247 – 249Combined sources3
Beta strandi258 – 260Combined sources3
Beta strandi267 – 275Combined sources9
Beta strandi281 – 286Combined sources6
Helixi290 – 304Combined sources15
Beta strandi313 – 315Combined sources3
Beta strandi326 – 335Combined sources10
Helixi336 – 346Combined sources11
Helixi349 – 364Combined sources16
Helixi369 – 382Combined sources14
Beta strandi395 – 397Combined sources3
Beta strandi403 – 405Combined sources3
Helixi406 – 417Combined sources12
Beta strandi418 – 421Combined sources4
Helixi422 – 428Combined sources7
Helixi437 – 440Combined sources4
Helixi441 – 443Combined sources3
Turni451 – 455Combined sources5
Beta strandi457 – 459Combined sources3
Beta strandi466 – 473Combined sources8
Beta strandi480 – 487Combined sources8
Beta strandi490 – 492Combined sources3
Helixi495 – 508Combined sources14

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP39045.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni146 – 319Absent in class-A beta-lactamasesAdd BLAST174

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)DescriptionActionsGraphical viewLength
Sequence conflicti100 – 101MK → GV AA sequence (PubMed:7305936).Curated2

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.
PIRiS22409.

3D structure databases

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

Chemistry databases

BindingDBiP39045.
ChEMBLiCHEMBL6016.

Protein family/group databases

MEROPSiS13.002.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00219.
BRENDAi3.4.16.4. 9774.
SABIO-RKP39045.

Miscellaneous databases

EvolutionaryTraceiP39045.

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.
ProtoNetiSearch...

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 2, 2016
This is version 98 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.