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- PDB-7s5j: Solution NMR structure of substrate bound peptidase domain from PCAT1 -

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Basic information

Entry
Database: PDB / ID: 7s5j
TitleSolution NMR structure of substrate bound peptidase domain from PCAT1
Components
  • CtA peptide
  • Peptidase C39
KeywordsPEPTIDE BINDING PROTEIN / C39 peptidase domain CtA substrate
Function / homology
Function and homology information


ABC-type bacteriocin transporter activity / ABC-type oligopeptide transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Cysteine proteinases / Cathepsin B; Chain A / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / Cysteine proteinases / Cathepsin B; Chain A / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
ABC-type bacteriocin transporter / Bacteriocin-type signal sequence-containing protein
Similarity search - Component
Biological speciesHungateiclostridium thermocellum (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsBhattacharya, S. / Palillo, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1P41GM118302-01A1 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1.
Authors: Bhattacharya, S. / Palillo, A.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase C39
B: CtA peptide


Theoretical massNumber of molelcules
Total (without water)19,3082
Polymers19,3082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2170 Å2
ΔGint-16 kcal/mol
Surface area10110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidase C39


Mass: 16635.389 Da / Num. of mol.: 1 / Fragment: N-terminal residues, 1-148 / Mutation: C24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0534 / Plasmid: PMCSG20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: A3DCU1
#2: Protein/peptide CtA peptide


Mass: 2672.960 Da / Num. of mol.: 1 / Fragment: sequence database residues 7-30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0535 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) RIL / References: UniProt: A3DCU2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D HNCA
161isotropic23D HNCO
171isotropic13D (H)CCH-COSY
1111isotropic23D (H)CCH-TOCSY
1101isotropic43D 1H-13C NOESY aliphatic
191isotropic43D 1H-13C NOESY aromatic
1121isotropic43D 1H-15N NOESY
1131isotropic42D f1,f2 C13/N15 filtered NOESY
1141isotropic42D f2 C13/N15 filtered NOESY
1192isotropic52D 1H-15N HSQC
1182isotropic52D 1H-13C HSQC aliphatic
1172isotropic52D 1H-13C HSQC aromatic
1162isotropic63D HNCA
1152isotropic53D HNCO
1202isotropic63D (H)CCH-COSY
1212isotropic63D (H)CCH-TOCSY
1222isotropic53D 1H-13C NOESY aliphatic
1232isotropic63D 1H-15N NOESY
1242isotropic53D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1140 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 255 uM CtA(5-37) peptide, 50 mM sodium phosphate, 150 mM sodium chloride, 5 mM DTT, 95% H2O/5% D2O15N/13C-labeled Sample95% H2O/5% D2O
solution2298 uM C39 peptidase domain, 184 uM [U-100% 13C; U-100% 15N] CtA(5-37) peptide, 50 mM sodium phosphate, 150 mM sodium chloride, 5 mM DTT, 95% H2O/5% D2O15N/13C-labeled Sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
140 uMC39 peptidase domain[U-100% 13C; U-100% 15N]1
255 uMCtA(5-37) peptidenatural abundance1
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
298 uMC39 peptidase domainnatural abundance2
184 uMCtA(5-37) peptide[U-100% 13C; U-100% 15N]2
50 mMsodium phosphatenatural abundance2
150 mMsodium chloridenatural abundance2
5 mMDTTnatural abundance2
Sample conditionsIonic strength: 150 mM NaCl mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE5001TXI CryoProbe
Bruker AVANCE III HDBrukerAVANCE III HD7002QCI CryoProbe
Bruker AVANCE III HDBrukerAVANCE III HD8005TCI CryoProbe
Bruker AVANCEBrukerAVANCE8006TXI CryoProbe
Bruker AVANCEBrukerAVANCE9004TCI CryoProbe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1, 3.5Bruker Biospincollection
TopSpin2.1, 3.5Bruker Biospinprocessing
CARA1.5Keller and Wuthrichchemical shift assignment
CARA1.5Keller and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
ARIA3.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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