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P15555

- DAC_STRSR

UniProt

P15555 - DAC_STRSR

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Protein

D-alanyl-D-alanine carboxypeptidase

Gene
N/A
Organism
Streptomyces sp. (strain R61)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

Functioni

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 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.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei93 – 931Acyl-ester intermediate
Binding sitei316 – 3161Substrate

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
Complete GO annotation...

Keywords - Molecular functioni

Carboxypeptidase, Hydrolase, Protease

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

UniPathwayiUPA00219.

Protein family/group databases

MEROPSiS12.001.

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine carboxypeptidase (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
OrganismiStreptomyces sp. (strain R61)
Taxonomic identifieri31952 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptomycineaeStreptomycetaceaeStreptomyces

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3131Add
BLAST
Chaini32 – 380349D-alanyl-D-alanine carboxypeptidasePRO_0000017050Add
BLAST
Propeptidei381 – 40626PRO_0000017051Add
BLAST

Structurei

Secondary structure

1
406
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi39 – 5113
Beta strandi55 – 639
Beta strandi66 – 7510
Turni77 – 793
Beta strandi88 – 903
Helixi92 – 943
Helixi95 – 10814
Helixi118 – 1214
Beta strandi125 – 1273
Helixi133 – 1375
Helixi147 – 1504
Beta strandi151 – 1533
Helixi154 – 1618
Helixi168 – 1769
Beta strandi181 – 1833
Helixi192 – 20615
Helixi210 – 2178
Turni218 – 2236
Beta strandi238 – 2403
Turni263 – 2653
Helixi266 – 2683
Helixi275 – 28612
Helixi293 – 2997
Beta strandi303 – 3064
Beta strandi309 – 3113
Beta strandi316 – 3194
Beta strandi325 – 3339
Beta strandi336 – 3427
Beta strandi346 – 35813
Helixi360 – 37415

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP15555.
SMRiP15555. Positions 32-378.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP15555.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni151 – 1544Substrate binding
Regioni190 – 1923Substrate binding
Regioni330 – 3323Substrate binding
Regioni357 – 3582Substrate binding

Sequence similaritiesi

Belongs to the peptidase S12 family.Curated

Keywords - Domaini

Signal

Family and domain databases

Gene3Di3.40.710.10. 1 hit.
InterProiIPR001466. Beta-lactam-related.
IPR012338. Beta-lactam/transpept-like.
[Graphical view]
PfamiPF00144. Beta-lactamase. 1 hit.
[Graphical view]
SUPFAMiSSF56601. SSF56601. 1 hit.

Sequencei

Sequence statusi: Complete.

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

P15555-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MVSGTVGRGT ALGAVLLALL AVPAQAGTAA AADLPAPDDT GLQAVLHTAL
60 70 80 90 100
SQGAPGAMVR VDDNGTIHQL SEGVADRATG RAITTTDRFR VGSVTKSFSA
110 120 130 140 150
VVLLQLVDEG KLDLDASVNT YLPGLLPDDR ITVRQVMSHR SGLYDYTNDM
160 170 180 190 200
FAQTVPGFES VRNKVFSYQD LITLSLKHGV TNAPGAAYSY SNTNFVVAGM
210 220 230 240 250
LIEKLTGHSV ATEYQNRIFT PLNLTDTFYV HPDTVIPGTH ANGYLTPDEA
260 270 280 290 300
GGALVDSTEQ TVSWAQSAGA VISSTQDLDT FFSALMSGQL MSAAQLAQMQ
310 320 330 340 350
QWTTVNSTQG YGLGLRRRDL SCGISVYGHT GTVQGYYTYA FASKDGKRSV
360 370 380 390 400
TALANTSNNV NVLNTMARTL ESAFCGKPTT AKLRSATSSA TTVERHEDIA

PGIARD
Length:406
Mass (Da):42,917
Last modified:February 1, 1996 - v2
Checksum:iC2C77B53A29099E9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X05109 Genomic DNA. Translation: CAA28756.1.
X55810 Genomic DNA. Translation: CAB97254.1.
PIRiS48220.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X05109 Genomic DNA. Translation: CAA28756.1 .
X55810 Genomic DNA. Translation: CAB97254.1 .
PIRi S48220.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1CEF X-ray 2.04 A 32-380 [» ]
1CEG X-ray 1.80 A 32-380 [» ]
1HVB X-ray 1.17 A 32-380 [» ]
1IKG X-ray 1.90 A 32-380 [» ]
1IKI X-ray 1.25 A 32-380 [» ]
1MPL X-ray 1.12 A 32-380 [» ]
1PW1 X-ray 1.20 A 32-380 [» ]
1PW8 X-ray 1.30 A 32-380 [» ]
1PWC X-ray 1.10 A 32-380 [» ]
1PWD X-ray 1.20 A 32-380 [» ]
1PWG X-ray 1.07 A 32-380 [» ]
1SCW X-ray 1.13 A 32-380 [» ]
1SDE X-ray 1.15 A 32-378 [» ]
1YQS X-ray 1.05 A 32-380 [» ]
2PTE model - E 32-380 [» ]
3PTE X-ray 1.60 A 32-380 [» ]
ProteinModelPortali P15555.
SMRi P15555. Positions 32-378.
ModBasei Search...
MobiDBi Search...

Chemistry

ChEMBLi CHEMBL3350.
DrugBanki DB00456. Cefalotin.

Protein family/group databases

MEROPSi S12.001.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Enzyme and pathway databases

UniPathwayi UPA00219 .

Miscellaneous databases

EvolutionaryTracei P15555.

Family and domain databases

Gene3Di 3.40.710.10. 1 hit.
InterProi IPR001466. Beta-lactam-related.
IPR012338. Beta-lactam/transpept-like.
[Graphical view ]
Pfami PF00144. Beta-lactamase. 1 hit.
[Graphical view ]
SUPFAMi SSF56601. SSF56601. 1 hit.
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiDAC_STRSR
AccessioniPrimary (citable) accession number: P15555
Secondary accession number(s): Q06656
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: February 1, 1996
Last modified: October 29, 2014
This is version 99 of the entry and version 2 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