data_17122 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution-state NMR Investigations of Triosephosphate Isomerase Active Site Loop Motion: Ligand Release in Relation to Active Site Loop Dynamics ; _BMRB_accession_number 17122 _BMRB_flat_file_name bmr17122.str _Entry_type new _Submission_date 2010-08-11 _Accession_date 2010-08-11 _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 Rozovsky Sharon . . 2 Jogl Gerwald . . 3 Tong Liang . . 4 McDermott Ann E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count kinetic_rates 2 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-10 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution-state NMR Investigations of Triosephosphate Isomerase Active Site Loop Motion: Ligand Release in Relation to Active Site Loop Dynamics' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 11419952 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Rozovsky Sharon . . 2 Jogl Gerwald . . 3 Tong Liang . . 4 McDermott Ann E. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 310 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 271 _Page_last 280 _Year 2001 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name TIM/G3P _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label TIM $TIM G3P $G3P stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TIM _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common TIM _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 247 _Mol_residue_sequence ; ARTFFVGGNFKLNGSKQSIK EIVERLNTASIPENVEVVIC PPATYLDYSVSLVKKPQVTV GAQNAYLKASGAFTGENSVD QIKDVGAKYVILGHSERRSY FHEDDKFIADKTKFALGQGV GVILCIGETLEEKKAGKTLD VVERQLNAVLEEVKDFTNVV VAYEPVWXIGTGLAATPEDA QDIHASIRKFLASKLGDKAA SELRILYGGSANGSNAVTFK DKADVDGFLVGGASLKPEFV DIINSRN ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 ARG 3 THR 4 PHE 5 PHE 6 VAL 7 GLY 8 GLY 9 ASN 10 PHE 11 LYS 12 LEU 13 ASN 14 GLY 15 SER 16 LYS 17 GLN 18 SER 19 ILE 20 LYS 21 GLU 22 ILE 23 VAL 24 GLU 25 ARG 26 LEU 27 ASN 28 THR 29 ALA 30 SER 31 ILE 32 PRO 33 GLU 34 ASN 35 VAL 36 GLU 37 VAL 38 VAL 39 ILE 40 CYS 41 PRO 42 PRO 43 ALA 44 THR 45 TYR 46 LEU 47 ASP 48 TYR 49 SER 50 VAL 51 SER 52 LEU 53 VAL 54 LYS 55 LYS 56 PRO 57 GLN 58 VAL 59 THR 60 VAL 61 GLY 62 ALA 63 GLN 64 ASN 65 ALA 66 TYR 67 LEU 68 LYS 69 ALA 70 SER 71 GLY 72 ALA 73 PHE 74 THR 75 GLY 76 GLU 77 ASN 78 SER 79 VAL 80 ASP 81 GLN 82 ILE 83 LYS 84 ASP 85 VAL 86 GLY 87 ALA 88 LYS 89 TYR 90 VAL 91 ILE 92 LEU 93 GLY 94 HIS 95 SER 96 GLU 97 ARG 98 ARG 99 SER 100 TYR 101 PHE 102 HIS 103 GLU 104 ASP 105 ASP 106 LYS 107 PHE 108 ILE 109 ALA 110 ASP 111 LYS 112 THR 113 LYS 114 PHE 115 ALA 116 LEU 117 GLY 118 GLN 119 GLY 120 VAL 121 GLY 122 VAL 123 ILE 124 LEU 125 CYS 126 ILE 127 GLY 128 GLU 129 THR 130 LEU 131 GLU 132 GLU 133 LYS 134 LYS 135 ALA 136 GLY 137 LYS 138 THR 139 LEU 140 ASP 141 VAL 142 VAL 143 GLU 144 ARG 145 GLN 146 LEU 147 ASN 148 ALA 149 VAL 150 LEU 151 GLU 152 GLU 153 VAL 154 LYS 155 ASP 156 PHE 157 THR 158 ASN 159 VAL 160 VAL 161 VAL 162 ALA 163 TYR 164 GLU 165 PRO 166 VAL 167 TRP 168 FTR 169 ILE 170 GLY 171 THR 172 GLY 173 LEU 174 ALA 175 ALA 176 THR 177 PRO 178 GLU 179 ASP 180 ALA 181 GLN 182 ASP 183 ILE 184 HIS 185 ALA 186 SER 187 ILE 188 ARG 189 LYS 190 PHE 191 LEU 192 ALA 193 SER 194 LYS 195 LEU 196 GLY 197 ASP 198 LYS 199 ALA 200 ALA 201 SER 202 GLU 203 LEU 204 ARG 205 ILE 206 LEU 207 TYR 208 GLY 209 GLY 210 SER 211 ALA 212 ASN 213 GLY 214 SER 215 ASN 216 ALA 217 VAL 218 THR 219 PHE 220 LYS 221 ASP 222 LYS 223 ALA 224 ASP 225 VAL 226 ASP 227 GLY 228 PHE 229 LEU 230 VAL 231 GLY 232 GLY 233 ALA 234 SER 235 LEU 236 LYS 237 PRO 238 GLU 239 PHE 240 VAL 241 ASP 242 ILE 243 ILE 244 ASN 245 SER 246 ARG 247 ASN 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 16565 WT_yeast_TIM_homodimer 100.00 248 98.79 99.60 2.75e-175 BMRB 16566 WT_yeast_TIM_homodimer 100.00 248 98.79 99.60 2.75e-175 PDB 1I45 "Yeast Triosephosphate Isomerase (Mutant)" 100.00 248 99.19 99.19 1.09e-174 PDB 1NEY "Triosephosphate Isomerase In Complex With Dhap" 100.00 247 99.19 99.19 1.43e-174 PDB 1NF0 "Triosephosphate Isomerase In Complex With Dhap" 100.00 247 99.19 99.19 1.43e-174 PDB 1YPI "Structure Of Yeast Triosephosphate Isomerase At 1.9- Angstroms Resolution" 100.00 247 98.79 99.60 5.77e-175 PDB 2YPI "Crystallographic Analysis Of The Complex Between Triosephosphate Isomerase And 2-Phosphoglycolate At 2.5- Angstroms Resolution." 100.00 247 98.79 99.60 5.77e-175 PDB 3YPI "Electrophilic Catalysis In Triosephosphase Isomerase: The Role Of Histidine-95" 100.00 247 98.38 99.19 5.87e-174 PDB 4FF7 "Structure Of C126s Mutant Of Saccharomyces Cerevisiae Triosephosphate Isomerase" 100.00 248 98.38 99.19 9.42e-174 PDB 7TIM "Structure Of The Triosephosphate Isomerase- Phosphoglycolohydroxamate Complex: An Analogue Of The Intermediate On The Reaction " 100.00 247 98.79 99.60 5.77e-175 DBJ GAA22287 "K7_Tpi1p [Saccharomyces cerevisiae Kyokai no. 7]" 100.00 248 98.79 99.60 2.75e-175 EMBL CAA89080 "Tpi1p [Saccharomyces cerevisiae]" 100.00 248 98.79 99.60 2.75e-175 EMBL CAY78558 "Tpi1p [Saccharomyces cerevisiae EC1118]" 100.00 248 98.79 99.60 2.75e-175 GB AAA88757 "triose phosphate isomerase [Saccharomyces cerevisiae]" 100.00 248 98.79 99.60 2.75e-175 GB AAS55980 "YDR050C [Saccharomyces cerevisiae]" 100.00 248 98.79 99.60 2.75e-175 GB AHY75046 "Tpi1p [Saccharomyces cerevisiae YJM993]" 100.00 248 98.79 99.60 2.75e-175 GB AJP37778 "Tpi1p [Saccharomyces cerevisiae YJM1078]" 100.00 248 98.79 99.60 2.75e-175 GB AJU57896 "Tpi1p [Saccharomyces cerevisiae YJM189]" 100.00 248 98.79 99.60 2.75e-175 REF NP_010335 "triose-phosphate isomerase TPI1 [Saccharomyces cerevisiae S288c]" 100.00 248 98.79 99.60 2.75e-175 SP P00942 "RecName: Full=Triosephosphate isomerase; Short=TIM; AltName: Full=Triose-phosphate isomerase" 100.00 248 98.79 99.60 2.75e-175 TPG DAA11897 "TPA: triose-phosphate isomerase TPI1 [Saccharomyces cerevisiae S288c]" 100.00 248 98.79 99.60 2.75e-175 stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_FTR _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common FLUOROTRYPTOPHANE _BMRB_code . _PDB_code FTR _Standard_residue_derivative . _Molecular_mass 222.216 _Mol_paramagnetic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 14:11:36 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD2 CD2 C . 0 . ? CE2 CE2 C . 0 . ? CE3 CE3 C . 0 . ? CD1 CD1 C . 0 . ? NE1 NE1 N . 0 . ? CZ2 CZ2 C . 0 . ? CZ3 CZ3 C . 0 . ? F F F . 0 . ? CH2 CH2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HE3 HE3 H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HZ2 HZ2 H . 0 . ? HH2 HH2 H . 0 . ? HXT HXT H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD2 ? ? DOUB CG CD1 ? ? DOUB CD2 CE2 ? ? SING CD2 CE3 ? ? SING CE2 NE1 ? ? SING CE2 CZ2 ? ? DOUB CE3 CZ3 ? ? SING CE3 HE3 ? ? SING CD1 NE1 ? ? SING CD1 HD1 ? ? SING NE1 HE1 ? ? DOUB CZ2 CH2 ? ? SING CZ2 HZ2 ? ? SING CZ3 F ? ? SING CZ3 CH2 ? ? SING CH2 HH2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ ############# # Ligands # ############# save_G3P _Saveframe_category ligand _Mol_type non-polymer _Name_common "G3P (SN-GLYCEROL-3-PHOSPHATE)" _BMRB_code . _PDB_code G3P _Molecular_mass 172.074 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic no _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 14:14:34 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O1 O1 O . 0 . ? C1 C1 C . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? C3 C3 C . 0 . ? O1P O1P O . 0 . ? O4P O4P O . 0 . ? O2P O2P O . 0 . ? O3P O3P O . 0 . ? P P P . 0 . ? HO1 HO1 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H2 H2 H . 0 . ? HO2 HO2 H . 0 . ? H31 H31 H . 0 . ? H32 H32 H . 0 . ? HOP3 HOP3 H . 0 . ? HOP4 HOP4 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING O1 C1 ? ? SING C1 C2 ? ? SING C2 O2 ? ? SING C2 C3 ? ? SING C3 O1P ? ? SING O1P P ? ? SING O4P P ? ? DOUB O2P P ? ? SING O3P P ? ? SING O1 HO1 ? ? SING C1 H11 ? ? SING C1 H12 ? ? SING C2 H2 ? ? SING O2 HO2 ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING O3P HOP3 ? ? SING O4P HOP4 ? ? stop_ _Mol_thiol_state 'not present' _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $TIM 'Baker's yeast' 4932 Eukaryota Fungi Saccharomyces cerevisiae 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 $TIM 'purified from the natural source' . . . . . 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 $TIM 1.2 mM 'natural abundance' Tris-HCl 50 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' $G3P 0-10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details 'G3P was titrated into solution' loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $TIM 2.1 mM . . 'natural abundance' Tris-HCl 50 mM . . 'natural abundance' 'sodium chloride' 50 mM . . 'natural abundance' $G3P . mM 0 5.75 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_MOLSCRIPT _Saveframe_category software _Name MOLSCRIPT _Version . loop_ _Vendor _Address _Electronic_address 'Kraulis, 1991' . . stop_ loop_ _Task visualization stop_ _Details . save_ save_RASTER3D _Saveframe_category software _Name RASTER3D _Version . loop_ _Vendor _Address _Electronic_address 'Merritt & Bacon, 1997' . . stop_ loop_ _Task visualization stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 300 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 400 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_19F_NMR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '19F NMR' _Sample_label $sample_1 save_ save_19F_NMR_2 _Saveframe_category NMR_applied_experiment _Experiment_name '19F NMR' _Sample_label $sample_1 save_ save_31P_NMR_3 _Saveframe_category NMR_applied_experiment _Experiment_name '31P NMR' _Sample_label $sample_2 save_ save_31P_NMR_4 _Saveframe_category NMR_applied_experiment _Experiment_name '31P NMR' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 273 . K pH 6.8 . pH pressure ambient . atm 'ionic strength' 50 . mM stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303 . K pH 6.8 . pH pressure ambient . atm 'ionic strength' 50 . mM stop_ save_