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P15555 (DAC_STRSR) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 97. 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
OrganismStreptomyces sp. (strain R61)
Taxonomic identifier31952 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptomycineaeStreptomycetaceaeStreptomyces

Protein attributes

Sequence length406 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).

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.

Pathway

Cell wall biogenesis; peptidoglycan biosynthesis.

Subcellular location

Secreted.

Sequence similarities

Belongs to the peptidase S12 family.

Ontologies

Keywords
   Biological processCell shape
Cell wall biogenesis/degradation
Peptidoglycan synthesis
   Cellular componentSecreted
   DomainSignal
   Molecular functionCarboxypeptidase
Hydrolase
Protease
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processpeptidoglycan biosynthetic process

Inferred from electronic annotation. Source: UniProtKB-UniPathway

regulation of cell shape

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentextracellular region

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionserine-type D-Ala-D-Ala carboxypeptidase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3131
Chain32 – 380349D-alanyl-D-alanine carboxypeptidase
PRO_0000017050
Propeptide381 – 40626
PRO_0000017051

Regions

Region151 – 1544Substrate binding
Region190 – 1923Substrate binding
Region330 – 3323Substrate binding
Region357 – 3582Substrate binding

Sites

Active site931Acyl-ester intermediate
Binding site3161Substrate

Secondary structure

........................................................ 406
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P15555 [UniParc].

Last modified February 1, 1996. Version 2.
Checksum: C2C77B53A29099E9

FASTA40642,917
        10         20         30         40         50         60 
MVSGTVGRGT ALGAVLLALL AVPAQAGTAA AADLPAPDDT GLQAVLHTAL SQGAPGAMVR 

        70         80         90        100        110        120 
VDDNGTIHQL SEGVADRATG RAITTTDRFR VGSVTKSFSA VVLLQLVDEG KLDLDASVNT 

       130        140        150        160        170        180 
YLPGLLPDDR ITVRQVMSHR SGLYDYTNDM FAQTVPGFES VRNKVFSYQD LITLSLKHGV 

       190        200        210        220        230        240 
TNAPGAAYSY SNTNFVVAGM LIEKLTGHSV ATEYQNRIFT PLNLTDTFYV HPDTVIPGTH 

       250        260        270        280        290        300 
ANGYLTPDEA GGALVDSTEQ TVSWAQSAGA VISSTQDLDT FFSALMSGQL MSAAQLAQMQ 

       310        320        330        340        350        360 
QWTTVNSTQG YGLGLRRRDL SCGISVYGHT GTVQGYYTYA FASKDGKRSV TALANTSNNV 

       370        380        390        400 
NVLNTMARTL ESAFCGKPTT AKLRSATSSA TTVERHEDIA PGIARD 

« Hide

References

[1]"Primary structure of the Streptomyces R61 extracellular DD-peptidase. 1. Cloning into Streptomyces lividans and nucleotide sequence of the gene."
Duez C., Piron-Fraipont C., Joris B., Dusart J., Urdea M.S., Martial J.A., Frere J.-M., Ghuysen J.-M.
Eur. J. Biochem. 162:509-518(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Primary structure of the Streptomyces R61 extracellular DD-peptidase. 1. Cloning into Streptomyces lividans and nucleotide sequence of the gene."
Duez C., Piron-Fraipont C., Joris B., Dusart J., Urdea M.S., Martial J.A., Frere J.-M., Ghuysen J.-M.
Eur. J. Biochem. 224:1079-1079(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
[3]"Primary structure of the Streptomyces R61 extracellular DD-peptidase. 2. Amino acid sequence data."
Joris B., Jacques P., Frere J.-M., Ghuysen J.-M., van Beeumen J.
Eur. J. Biochem. 162:519-524(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: PARTIAL PROTEIN SEQUENCE.
[4]"Transcriptional analysis of the DD-peptidase/penicillin-binding protein-encoding dac gene of Streptomyces R61: use of the promoter and signal sequences in a secretion vector."
Piron-Fraipont C., Lenzini M.V., Dusart J., Ghuysen J.-M.
Mol. Gen. Genet. 223:114-120(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-91.
[5]"Different modes of vancomycin and D-alanyl-D-alanine peptidase binding to cell wall peptide and a possible role for the vancomycin resistance protein."
Knox J.R., Pratt R.F.
Antimicrob. Agents Chemother. 34:1342-1347(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: 3D-STRUCTURE MODELING.
[6]"2.8-A structure of penicillin-sensitive D-alanyl carboxypeptidase-transpeptidase from Streptomyces R61 and complexes with beta-lactams."
Kelly J.A., Knox J.R., Moews P.C., Hite G.J., Bartolone J.B., Zhao H., Joris B., Frere J.-M., Ghuysen J.-M.
J. Biol. Chem. 260:6449-6458(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
[7]"The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6-A resolution."
Kelly J.A., Kuzin A.P.
J. Mol. Biol. 254:223-236(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
[8]"Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins."
McDonough M.A., Anderson J.W., Silvaggi N.R., Pratt R.F., Knox J.R., Kelly J.A.
J. Mol. Biol. 322:111-122(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 32-380 IN COMPLEX WITH SUBSTRATES.
[9]"The crystal structure of phosphonate-inhibited D-Ala-D-Ala peptidase reveals an analogue of a tetrahedral transition state."
Silvaggi N.R., Anderson J.W., Brinsmade S.R., Pratt R.F., Kelly J.A.
Biochemistry 42:1199-1208(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.12 ANGSTROMS) OF 32-380 IN COMPLEX WITH SUBSTRATES.
[10]"Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a 'perfect penicillin'."
Silvaggi N.R., Josephine H.R., Kuzin A.P., Nagarajan R., Pratt R.F., Kelly J.A.
J. Mol. Biol. 345:521-533(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.07 ANGSTROMS) OF 32-380 IN COMPLEX WITH SUBSTRATE ANALOG.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X05109 Genomic DNA. Translation: CAA28756.1.
X55810 Genomic DNA. Translation: CAB97254.1.
PIRS48220.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1CEFX-ray2.04A32-380[»]
1CEGX-ray1.80A32-380[»]
1HVBX-ray1.17A32-380[»]
1IKGX-ray1.90A32-380[»]
1IKIX-ray1.25A32-380[»]
1MPLX-ray1.12A32-380[»]
1PW1X-ray1.20A32-380[»]
1PW8X-ray1.30A32-380[»]
1PWCX-ray1.10A32-380[»]
1PWDX-ray1.20A32-380[»]
1PWGX-ray1.07A32-380[»]
1SCWX-ray1.13A32-380[»]
1SDEX-ray1.15A32-378[»]
1YQSX-ray1.05A32-380[»]
2PTEmodel-E32-380[»]
3PTEX-ray1.60A32-380[»]
ProteinModelPortalP15555.
SMRP15555. Positions 32-378.
ModBaseSearch...
MobiDBSearch...

Chemistry

ChEMBLCHEMBL3350.
DrugBankDB00456. Cefalotin.

Protein family/group databases

MEROPSS12.001.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayUPA00219.

Family and domain databases

Gene3D3.40.710.10. 1 hit.
InterProIPR001466. Beta-lactam-related.
IPR012338. Beta-lactam/transpept-like.
[Graphical view]
PfamPF00144. Beta-lactamase. 1 hit.
[Graphical view]
SUPFAMSSF56601. SSF56601. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP15555.

Entry information

Entry nameDAC_STRSR
AccessionPrimary (citable) accession number: P15555
Secondary accession number(s): Q06656
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: February 1, 1996
Last modified: July 9, 2014
This is version 97 of the entry and version 2 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