data_10116 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Confirmation of the Denatured Structure of Pyrrolidone Carboxyl Peptidase under Non denaturing Conditions: Helix Propensity of wild-type H6-peptide ; _BMRB_accession_number 10116 _BMRB_flat_file_name bmr10116.str _Entry_type original _Submission_date 2007-02-16 _Accession_date 2007-02-17 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Umezaki Taro . . 2 Iimura Satoshi . . 3 Noda Yasuo . . 4 Segawa Shin-ichi . . 5 Yutani Katsuhide . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 87 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-06-27 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 10117 'the substitution of Pro for Ala12' stop_ _Original_release_date 2008-06-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The confirmation of the denatured structure of pyrrolidone carboxyl peptidase under nondenaturing conditions: difference in helix propensity of two synthetic peptides with single amino acid substitution. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17979195 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Umezaki Taro . . 2 Iimura Satoshi . . 3 Noda Yasuo . . 4 Segawa Shin-ichi . . 5 Yutani Katsuhide . . stop_ _Journal_abbreviation Proteins _Journal_volume 71 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 737 _Page_last 742 _Year 2008 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_citation_2 _Saveframe_category citation _Citation_full . _Citation_title ; Characterization of the denatured structure of pyrrolidone carboxyl peptidase from a hyperthermophile under nondenaturing conditions: role of the C-terminal alpha-helix of the protein in folding and stability. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17309236 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Iimura Satoshi . . 2 Umezaki Taro . . 3 Takeuchi Makoto . . 4 Mizuguchi Mineyuki . . 5 Yagi Hiromasa . . 6 Ogasahara Kyoko . . 7 Akutsu Hideo . . 8 Noda Yasuo . . 9 Segawa Shin-ichi . . 10 Yutani Katsuhide . . stop_ _Journal_abbreviation Biochemistry _Journal_name_full . _Journal_volume 46 _Journal_issue 12 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 3664 _Page_last 3672 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'PCP homo tetramer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'subunit 1' $wild-type_H6-peptide 'subunit 2' $wild-type_H6-peptide 'subunit 3' $wild-type_H6-peptide 'subunit 4' $wild-type_H6-peptide stop_ _System_molecular_weight 91200 _System_physical_state native _System_oligomer_state 'protein-protein complex' _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'subunit 1' 1 'subunit 2' 1 'subunit 3' 1 'subunit 4' stop_ loop_ _Biological_function 'removal of N-terminal pyroglutamic acid from polypeptide' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_wild-type_H6-peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'wild-type H6-peptide' _Molecular_mass 2023 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence SYEMELEAVKVAIEVALE loop_ _Residue_seq_code _Residue_label 1 SER 2 TYR 3 GLU 4 MET 5 GLU 6 LEU 7 GLU 8 ALA 9 VAL 10 LYS 11 VAL 12 ALA 13 ILE 14 GLU 15 VAL 16 ALA 17 LEU 18 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-08 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 10052 "pyrrolidone carboxyl peptidase cys-free mutant" 100.00 208 100.00 100.00 1.05e+00 PDB 1IOF "X-Ray Crystalline Structures Of Pyrrolidone Carboxyl Peptidase From A Hyperthermophile, Pyrococcus Furiosus, And Its Cys-Free M" 94.44 208 100.00 100.00 5.14e+00 PDB 1IOI "X-Ray Crystalline Structures Of Pyrrolidone Carboxyl Peptidase From A Hyperthermophile, Pyrococcus Furiosus, And Its Cys-Free M" 100.00 208 100.00 100.00 1.05e+00 DBJ BAA32989 "pyrrolidone carboxyl peptidase [Pyrococcus furiosus]" 94.44 208 100.00 100.00 5.14e+00 GB AAL81423 "pyroglutamyl-peptidase i [Pyrococcus furiosus DSM 3638]" 94.44 208 100.00 100.00 5.14e+00 GB AFN04083 "pyrrolidone-carboxylate peptidase [Pyrococcus furiosus COM1]" 94.44 208 100.00 100.00 5.14e+00 REF WP_011012443 "pyrrolidone-carboxylate peptidase [Pyrococcus furiosus]" 94.44 208 100.00 100.00 5.14e+00 SP O73944 "RecName: Full=Pyrrolidone-carboxylate peptidase; AltName: Full=5-oxoprolyl-peptidase; AltName: Full=Pyroglutamyl-peptidase I; S" 94.44 208 100.00 100.00 5.14e+00 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Fraction $wild-type_H6-peptide 'Pyrococcus furiosus' 2261 Archaea . Pyrococcus furiosus no stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $wild-type_H6-peptide 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $wild-type_H6-peptide 0.7 mM . '2.2.2 trifluoroethanol-d2' 30 % . stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name xwinnmr _Version . loop_ _Task collection stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Task 'peak assignments' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _Sample_label $sample_1 save_ save_HOHAHA_2 _Saveframe_category NMR_applied_experiment _Experiment_name HOHAHA _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_1H-1H_NOESY _Saveframe_category NMR_applied_experiment _Experiment_name '1H-1H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_HOHAHA _Saveframe_category NMR_applied_experiment _Experiment_name HOHAHA _BMRB_pulse_sequence_accession_number . _Details . save_ save_DQF-COSY _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_condition_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 0.02 pH temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.015 external direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_wild-type_H6-peptide_30%TFE_pH7.0_25C _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '1H-1H NOESY' HOHAHA DQF-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $condition_1 _Chem_shift_reference_set_label $reference_1 _Mol_system_component_name 'subunit 1' _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 2 2 TYR HA H 4.56 0.01 1 2 2 2 TYR HB2 H 3.13 0.01 2 3 2 2 TYR HD1 H 6.88 0.01 3 4 2 2 TYR HE1 H 6.54 0.01 3 5 3 3 GLU H H 9.00 0.01 1 6 3 3 GLU HA H 4.03 0.01 1 7 3 3 GLU HB2 H 2.04 0.01 2 8 3 3 GLU HG2 H 2.42 0.01 2 9 3 3 GLU HG3 H 2.29 0.01 2 10 4 4 MET H H 7.98 0.01 1 11 4 4 MET HA H 4.33 0.01 1 12 4 4 MET HB2 H 2.16 0.01 2 13 4 4 MET HG2 H 2.70 0.01 2 14 4 4 MET HG3 H 2.61 0.01 2 15 5 5 GLU H H 8.36 0.01 1 16 5 5 GLU HA H 4.13 0.01 1 17 5 5 GLU HB2 H 2.16 0.01 1 18 5 5 GLU HB3 H 2.16 0.01 1 19 5 5 GLU HG2 H 2.41 0.01 2 20 5 5 GLU HG3 H 2.38 0.01 2 21 6 6 LEU H H 8.07 0.01 1 22 6 6 LEU HA H 4.16 0.01 1 23 6 6 LEU HB2 H 1.75 0.01 2 24 6 6 LEU HB3 H 1.64 0.01 2 25 6 6 LEU HG H 1.67 0.01 1 26 6 6 LEU HD1 H 0.92 0.01 2 27 6 6 LEU HD2 H 0.90 0.01 2 28 7 7 GLU H H 7.96 0.01 1 29 7 7 GLU HA H 4.07 0.01 1 30 7 7 GLU HB2 H 2.40 0.01 2 31 7 7 GLU HB3 H 2.15 0.01 2 32 8 8 ALA H H 7.81 0.01 1 33 8 8 ALA HA H 4.15 0.01 1 34 8 8 ALA HB H 1.55 0.01 1 35 9 9 VAL H H 7.80 0.01 1 36 9 9 VAL HA H 3.77 0.01 1 37 9 9 VAL HB H 2.27 0.01 1 38 9 9 VAL HG1 H 1.09 0.01 2 39 9 9 VAL HG2 H 0.99 0.01 2 40 10 10 LYS H H 7.92 0.01 1 41 10 10 LYS HA H 3.97 0.01 1 42 10 10 LYS HB2 H 1.98 0.01 2 43 10 10 LYS HB3 H 1.61 0.01 2 44 10 10 LYS HG2 H 1.42 0.01 2 45 10 10 LYS HD2 H 1.71 0.01 2 46 10 10 LYS HE2 H 2.97 0.01 2 47 11 11 VAL H H 7.81 0.01 1 48 11 11 VAL HA H 3.84 0.01 1 49 11 11 VAL HB H 2.18 0.01 1 50 11 11 VAL HG1 H 1.11 0.01 2 51 11 11 VAL HG2 H 1.00 0.01 2 52 12 12 ALA H H 7.81 0.01 1 53 12 12 ALA HA H 4.16 0.01 1 54 12 12 ALA HB H 1.55 0.01 1 55 13 13 ILE H H 8.19 0.01 1 56 13 13 ILE HA H 3.91 0.01 1 57 13 13 ILE HB H 1.99 0.01 1 58 13 13 ILE HG12 H 1.75 0.01 2 59 13 13 ILE HG13 H 1.20 0.01 2 60 13 13 ILE HG2 H 0.94 0.01 1 61 13 13 ILE HD1 H 0.85 0.01 1 62 14 14 GLU H H 8.08 0.01 1 63 14 14 GLU HA H 4.11 0.01 1 64 14 14 GLU HB2 H 2.21 0.01 2 65 14 14 GLU HB3 H 2.13 0.01 2 66 14 14 GLU HG2 H 2.53 0.01 2 67 14 14 GLU HG3 H 2.31 0.01 2 68 15 15 VAL H H 8.15 0.01 1 69 15 15 VAL HA H 4.04 0.01 1 70 15 15 VAL HB H 2.23 0.01 1 71 15 15 VAL HG1 H 1.07 0.01 2 72 15 15 VAL HG2 H 1.00 0.01 2 73 16 16 ALA H H 7.93 0.01 1 74 16 16 ALA HA H 4.35 0.01 1 75 16 16 ALA HB H 1.53 0.01 1 76 17 17 LEU H H 7.90 0.01 1 77 17 17 LEU HA H 4.39 0.01 1 78 17 17 LEU HB2 H 1.80 0.01 2 79 17 17 LEU HB3 H 1.68 0.01 2 80 17 17 LEU HG H 1.85 0.01 1 81 17 17 LEU HD1 H 0.96 0.01 2 82 17 17 LEU HD2 H 0.90 0.01 2 83 18 18 GLU H H 7.63 0.01 1 84 18 18 GLU HA H 4.13 0.01 1 85 18 18 GLU HB2 H 2.11 0.01 2 86 18 18 GLU HB3 H 2.02 0.01 2 87 18 18 GLU HG2 H 2.33 0.01 2 stop_ save_