data_18685 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Hydogen exchange rate of Adenylate kinase Leu58 amide proton, in complex with Ap5A ; _BMRB_accession_number 18685 _BMRB_flat_file_name bmr18685.str _Entry_type original _Submission_date 2012-08-30 _Accession_date 2012-08-30 _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 Aden Jorgen . . 2 Verma Abhinav . . 3 Schug Alexander . . 4 Wolf-Watz Magnus . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count H_exch_rates 1 stop_ loop_ _Data_type _Data_type_count "H exchange rates" 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-10-18 original author . stop_ _Original_release_date 2012-10-18 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Modulation of a Pre-existing Conformational Equilibrium Tunes Adenylate Kinase Activity.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22963267 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Aden Jorgen . . 2 Verma Abhinav . . 3 Schug Alexander . . 4 Wolf-Watz Magnus . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 134 _Journal_issue 40 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 16562 _Page_last 16570 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'adenylate kinase' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'adenylate kinase' $adenylate_kinase Ap5A $entity_AP5 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_adenylate_kinase _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common adenylate_kinase _Molecular_mass . _Mol_thiol_state 'not reported' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 214 _Mol_residue_sequence ; MRIILLGAPGAGKGTQAQFI MEKYGIPQISTGDMLRAAVK SGSELGKQAKDIMDAGKLVT DELVIALVKERIAQEDCRNG FLLDGFPRTIPQADAMKEAG INVDYVLEFDVPDELIVDRI VGRRVHAPSGRVYHVKFNPP KVEGKDDVTGEELTTRKDDQ EETVRKRLVEYHQMTAPLIG YYSKEAEAGNTKYAKVDGTK PVAEVRADLEKILG ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ARG 3 ILE 4 ILE 5 LEU 6 LEU 7 GLY 8 ALA 9 PRO 10 GLY 11 ALA 12 GLY 13 LYS 14 GLY 15 THR 16 GLN 17 ALA 18 GLN 19 PHE 20 ILE 21 MET 22 GLU 23 LYS 24 TYR 25 GLY 26 ILE 27 PRO 28 GLN 29 ILE 30 SER 31 THR 32 GLY 33 ASP 34 MET 35 LEU 36 ARG 37 ALA 38 ALA 39 VAL 40 LYS 41 SER 42 GLY 43 SER 44 GLU 45 LEU 46 GLY 47 LYS 48 GLN 49 ALA 50 LYS 51 ASP 52 ILE 53 MET 54 ASP 55 ALA 56 GLY 57 LYS 58 LEU 59 VAL 60 THR 61 ASP 62 GLU 63 LEU 64 VAL 65 ILE 66 ALA 67 LEU 68 VAL 69 LYS 70 GLU 71 ARG 72 ILE 73 ALA 74 GLN 75 GLU 76 ASP 77 CYS 78 ARG 79 ASN 80 GLY 81 PHE 82 LEU 83 LEU 84 ASP 85 GLY 86 PHE 87 PRO 88 ARG 89 THR 90 ILE 91 PRO 92 GLN 93 ALA 94 ASP 95 ALA 96 MET 97 LYS 98 GLU 99 ALA 100 GLY 101 ILE 102 ASN 103 VAL 104 ASP 105 TYR 106 VAL 107 LEU 108 GLU 109 PHE 110 ASP 111 VAL 112 PRO 113 ASP 114 GLU 115 LEU 116 ILE 117 VAL 118 ASP 119 ARG 120 ILE 121 VAL 122 GLY 123 ARG 124 ARG 125 VAL 126 HIS 127 ALA 128 PRO 129 SER 130 GLY 131 ARG 132 VAL 133 TYR 134 HIS 135 VAL 136 LYS 137 PHE 138 ASN 139 PRO 140 PRO 141 LYS 142 VAL 143 GLU 144 GLY 145 LYS 146 ASP 147 ASP 148 VAL 149 THR 150 GLY 151 GLU 152 GLU 153 LEU 154 THR 155 THR 156 ARG 157 LYS 158 ASP 159 ASP 160 GLN 161 GLU 162 GLU 163 THR 164 VAL 165 ARG 166 LYS 167 ARG 168 LEU 169 VAL 170 GLU 171 TYR 172 HIS 173 GLN 174 MET 175 THR 176 ALA 177 PRO 178 LEU 179 ILE 180 GLY 181 TYR 182 TYR 183 SER 184 LYS 185 GLU 186 ALA 187 GLU 188 ALA 189 GLY 190 ASN 191 THR 192 LYS 193 TYR 194 ALA 195 LYS 196 VAL 197 ASP 198 GLY 199 THR 200 LYS 201 PRO 202 VAL 203 ALA 204 GLU 205 VAL 206 ARG 207 ALA 208 ASP 209 LEU 210 GLU 211 LYS 212 ILE 213 LEU 214 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-04 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 18683 adenylate_kinase 100.00 214 100.00 100.00 1.83e-151 BMRB 18686 adenylate_kinase 100.00 214 99.53 99.53 1.26e-150 BMRB 18687 adenylate_kinase 100.00 214 100.00 100.00 1.83e-151 BMRB 19089 adenylate_kinase_wild_type 100.00 214 100.00 100.00 1.83e-151 BMRB 19090 adenylate_kinase_wild_type 100.00 214 100.00 100.00 1.83e-151 BMRB 19091 adenylate_kinase_wild_type 100.00 214 100.00 100.00 1.83e-151 BMRB 19092 adenylate_kinase_R156K_mutant 100.00 214 99.53 100.00 4.80e-151 BMRB 19093 adenylate_kinase_R156K_mutant 100.00 214 99.53 100.00 4.80e-151 BMRB 25353 Kinase 100.00 214 99.53 99.53 1.80e-150 BMRB 25357 Adenylate_Kinase_Y171W 100.00 214 99.53 100.00 3.27e-151 BMRB 25360 Adenylate_Kinase_P177A 100.00 214 99.53 99.53 1.80e-150 BMRB 25361 Adenylate_Kinase_Y171W 100.00 214 99.53 100.00 3.27e-151 BMRB 25362 Adenylate_Kinase_Y171W 100.00 214 99.53 100.00 3.27e-151 BMRB 4152 "Adenylate kinase" 100.00 214 100.00 100.00 1.83e-151 BMRB 4193 "Adenylate kinase" 100.00 214 100.00 100.00 1.83e-151 BMRB 4350 "Adenylate kinase from E. coli" 100.00 214 100.00 100.00 1.83e-151 PDB 1AKE "Structure Of The Complex Between Adenylate Kinase From Escherichia Coli And The Inhibitor Ap5a Refined At 1.9 Angstroms Resolut" 100.00 214 100.00 100.00 1.83e-151 PDB 1ANK "The Closed Conformation Of A Highly Flexible Protein: The Structure Of E. Cloi Adenylate Kinase With Bound Amp And Amppnp" 100.00 214 100.00 100.00 1.83e-151 PDB 1E4V "Mutant G10v Of Adenylate Kinase From E. Coli, Modified In The Gly-Loop" 100.00 214 99.53 99.53 2.70e-150 PDB 1E4Y "Mutant P9l Of Adenylate Kinase From E. Coli, Modified In The Gly-Loop" 100.00 214 99.07 99.07 4.64e-149 PDB 2ECK "Structure Of Phosphotransferase" 100.00 214 100.00 100.00 1.83e-151 PDB 3HPQ "Crystal Structure Of Wild-Type Adenylate Kinase From E. Coli, In Complex With Ap5a" 100.00 214 100.00 100.00 1.83e-151 PDB 3HPR "Crystal Structure Of V148g Adenylate Kinase From E. Coli, In Complex With Ap5a" 100.00 214 99.53 99.53 2.56e-150 PDB 3X2S "Crystal Structure Of Pyrene-conjugated Adenylate Kinase" 100.00 214 98.60 98.60 7.76e-149 PDB 4AKE "Adenylate Kinase" 100.00 214 100.00 100.00 1.83e-151 PDB 4JZK "Crystal Structure Of Adenylate Kinase Of E. Coli With Adp/amp Bound" 100.00 214 100.00 100.00 1.83e-151 PDB 4X8H "Crystal Structure Of E. Coli Adenylate Kinase P177a Mutant" 100.00 214 99.53 99.53 1.80e-150 PDB 4X8L "Crystal Structure Of E. Coli Adenylate Kinase P177a Mutant In Complex With Inhibitor Ap5a" 100.00 214 99.53 99.53 1.80e-150 PDB 4X8M "Crystal Structure Of E. Coli Adenylate Kinase Y171w Mutant" 100.00 214 99.53 100.00 3.27e-151 PDB 4X8O "Crystal Structure Of E. Coli Adenylate Kinase Y171w Mutant In Complex With Inhibitor Ap5a" 100.00 214 99.53 100.00 3.27e-151 DBJ BAA14303 "adenylate kinase [Escherichia coli K-12]" 50.00 107 100.00 100.00 1.13e-68 DBJ BAB33950 "adenylate kinase [Escherichia coli O157:H7 str. Sakai]" 100.00 214 100.00 100.00 1.83e-151 DBJ BAE76253 "adenylate kinase [Escherichia coli str. K12 substr. W3110]" 100.00 214 100.00 100.00 1.83e-151 DBJ BAG76023 "adenylate kinase [Escherichia coli SE11]" 100.00 214 100.00 100.00 1.83e-151 DBJ BAI23848 "adenylate kinase Adk [Escherichia coli O26:H11 str. 11368]" 100.00 214 100.00 100.00 1.83e-151 EMBL CAA26840 "unnamed protein product [Escherichia coli]" 100.00 214 100.00 100.00 1.83e-151 EMBL CAF33430 "adenylate kinase [Escherichia coli]" 71.96 154 100.00 100.00 3.88e-106 EMBL CAF33431 "adenylate kinase, partial [Escherichia coli]" 71.96 154 100.00 100.00 3.88e-106 EMBL CAF33432 "adenylate kinase, partial [Escherichia coli]" 71.96 154 100.00 100.00 3.88e-106 EMBL CAF33433 "adenylate kinase, partial [Escherichia coli]" 71.96 154 100.00 100.00 3.88e-106 GB AAA23461 "adk ORF [Escherichia coli]" 100.00 214 100.00 100.00 1.83e-151 GB AAB40228 "adenylate kinase [Escherichia coli]" 100.00 233 100.00 100.00 6.20e-152 GB AAC73576 "adenylate kinase [Escherichia coli str. K-12 substr. MG1655]" 100.00 214 100.00 100.00 1.83e-151 GB AAG54823 "adenylate kinase activity; pleiotropic effects on glycerol-3-phosphate acyltransferase activity [Escherichia coli O157:H7 str. " 100.00 214 100.00 100.00 1.83e-151 GB AAM94352 "adenylate kinase [Escherichia coli]" 79.91 171 100.00 100.00 1.31e-119 REF NP_308554 "adenylate kinase [Escherichia coli O157:H7 str. Sakai]" 100.00 214 100.00 100.00 1.83e-151 REF NP_415007 "adenylate kinase [Escherichia coli str. K-12 substr. MG1655]" 100.00 214 100.00 100.00 1.83e-151 REF NP_706367 "adenylate kinase [Shigella flexneri 2a str. 301]" 100.00 214 99.53 99.53 1.71e-150 REF WP_001220233 "MULTISPECIES: adenylate kinase [Proteobacteria]" 100.00 214 100.00 100.00 1.83e-151 REF WP_001220235 "adenylate kinase [Shigella flexneri]" 100.00 214 99.53 99.53 1.71e-150 SP A7ZIN4 "RecName: Full=Adenylate kinase; Short=AK; AltName: Full=ATP-AMP transphosphorylase; AltName: Full=ATP:AMP phosphotransferase; A" 100.00 214 100.00 100.00 1.83e-151 SP A7ZXD2 "RecName: Full=Adenylate kinase; Short=AK; AltName: Full=ATP-AMP transphosphorylase; AltName: Full=ATP:AMP phosphotransferase; A" 100.00 214 100.00 100.00 1.83e-151 SP B1IZC0 "RecName: Full=Adenylate kinase; Short=AK; AltName: Full=ATP-AMP transphosphorylase; AltName: Full=ATP:AMP phosphotransferase; A" 100.00 214 100.00 100.00 1.83e-151 SP B1LJN2 "RecName: Full=Adenylate kinase; Short=AK; AltName: Full=ATP-AMP transphosphorylase; AltName: Full=ATP:AMP phosphotransferase; A" 100.00 214 100.00 100.00 1.83e-151 SP B1XFR1 "RecName: Full=Adenylate kinase; Short=AK; AltName: Full=ATP-AMP transphosphorylase; AltName: Full=ATP:AMP phosphotransferase; A" 100.00 214 100.00 100.00 1.83e-151 stop_ save_ ############# # Ligands # ############# save_AP5 _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_AP5 (BIS(ADENOSINE)-5'-PENTAPHOSPHATE)" _BMRB_code AP5 _PDB_code AP5 _Molecular_mass 916.367 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons PA PA P . 0 . ? O1A O1A O . 0 . ? O2A O2A O . 0 . ? O3A O3A O . 0 . ? PB PB P . 0 . ? O1B O1B O . 0 . ? O2B O2B O . 0 . ? O3B O3B O . 0 . ? PG PG P . 0 . ? O1G O1G O . 0 . ? O2G O2G O . 0 . ? O3G O3G O . 0 . ? PD PD P . 0 . ? O1D O1D O . 0 . ? O2D O2D O . 0 . ? O3D O3D O . 0 . ? PE PE P . 0 . ? O1E O1E O . 0 . ? O2E O2E O . 0 . ? O5F O5F O . 0 . ? C5F C5F C . 0 . ? C4F C4F C . 0 . ? O4F O4F O . 0 . ? C3F C3F C . 0 . ? O3F O3F O . 0 . ? C2F C2F C . 0 . ? O2F O2F O . 0 . ? C1F C1F C . 0 . ? N9A N9A N . 0 . ? C8A C8A C . 0 . ? N7A N7A N . 0 . ? C5A C5A C . 0 . ? C6A C6A C . 0 . ? N6A N6A N . 0 . ? N1A N1A N . 0 . ? C2A C2A C . 0 . ? N3A N3A N . 0 . ? C4A C4A C . 0 . ? O5J O5J O . 0 . ? C5J C5J C . 0 . ? C4J C4J C . 0 . ? O4J O4J O . 0 . ? C3J C3J C . 0 . ? O3J O3J O . 0 . ? C2J C2J C . 0 . ? O2J O2J O . 0 . ? C1J C1J C . 0 . ? N9B N9B N . 0 . ? C8B C8B C . 0 . ? N7B N7B N . 0 . ? C5B C5B C . 0 . ? C6B C6B C . 0 . ? N6B N6B N . 0 . ? N1B N1B N . 0 . ? C2B C2B C . 0 . ? N3B N3B N . 0 . ? C4B C4B C . 0 . ? HOA2 HOA2 H . 0 . ? HOB2 HOB2 H . 0 . ? HOG2 HOG2 H . 0 . ? HOD2 HOD2 H . 0 . ? HOE2 HOE2 H . 0 . ? H51A H51A H . 0 . ? H52A H52A H . 0 . ? H4F H4F H . 0 . ? H3F H3F H . 0 . ? HO3A HO3A H . 0 . ? H2F H2F H . 0 . ? HO2A HO2A H . 0 . ? H1F H1F H . 0 . ? H8A H8A H . 0 . ? H61A H61A H . 0 . ? H62A H62A H . 0 . ? H2A H2A H . 0 . ? H51B H51B H . 0 . ? H52B H52B H . 0 . ? H4J H4J H . 0 . ? H3J H3J H . 0 . ? HO3B HO3B H . 0 . ? H2J H2J H . 0 . ? HO2B HO2B H . 0 . ? H1J H1J H . 0 . ? H8B H8B H . 0 . ? H61B H61B H . 0 . ? H62B H62B H . 0 . ? H2B H2B 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 DOUB PA O1A ? ? SING PA O2A ? ? SING PA O3A ? ? SING PA O5F ? ? SING O2A HOA2 ? ? SING O3A PB ? ? DOUB PB O1B ? ? SING PB O2B ? ? SING PB O3B ? ? SING O2B HOB2 ? ? SING O3B PG ? ? DOUB PG O1G ? ? SING PG O2G ? ? SING PG O3G ? ? SING O2G HOG2 ? ? SING O3G PD ? ? DOUB PD O1D ? ? SING PD O2D ? ? SING PD O3D ? ? SING O2D HOD2 ? ? SING O3D PE ? ? DOUB PE O1E ? ? SING PE O2E ? ? SING PE O5J ? ? SING O2E HOE2 ? ? SING O5F C5F ? ? SING C5F C4F ? ? SING C5F H51A ? ? SING C5F H52A ? ? SING C4F O4F ? ? SING C4F C3F ? ? SING C4F H4F ? ? SING O4F C1F ? ? SING C3F O3F ? ? SING C3F C2F ? ? SING C3F H3F ? ? SING O3F HO3A ? ? SING C2F O2F ? ? SING C2F C1F ? ? SING C2F H2F ? ? SING O2F HO2A ? ? SING C1F N9A ? ? SING C1F H1F ? ? SING N9A C8A ? ? SING N9A C4A ? ? DOUB C8A N7A ? ? SING C8A H8A ? ? SING N7A C5A ? ? SING C5A C6A ? ? DOUB C5A C4A ? ? SING C6A N6A ? ? DOUB C6A N1A ? ? SING N6A H61A ? ? SING N6A H62A ? ? SING N1A C2A ? ? DOUB C2A N3A ? ? SING C2A H2A ? ? SING N3A C4A ? ? SING O5J C5J ? ? SING C5J C4J ? ? SING C5J H51B ? ? SING C5J H52B ? ? SING C4J O4J ? ? SING C4J C3J ? ? SING C4J H4J ? ? SING O4J C1J ? ? SING C3J O3J ? ? SING C3J C2J ? ? SING C3J H3J ? ? SING O3J HO3B ? ? SING C2J O2J ? ? SING C2J C1J ? ? SING C2J H2J ? ? SING O2J HO2B ? ? SING C1J N9B ? ? SING C1J H1J ? ? SING N9B C8B ? ? SING N9B C4B ? ? DOUB C8B N7B ? ? SING C8B H8B ? ? SING N7B C5B ? ? SING C5B C6B ? ? DOUB C5B C4B ? ? SING C6B N6B ? ? DOUB C6B N1B ? ? SING N6B H61B ? ? SING N6B H62B ? ? SING N1B C2B ? ? DOUB C2B N3B ? ? SING C2B H2B ? ? SING N3B C4B ? ? stop_ _Mol_thiol_state . _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 $adenylate_kinase 'E. coli' 562 Bacteria . Escherichia coli 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 $adenylate_kinase 'recombinant technology' . Escherichia coli . pET 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 $adenylate_kinase 1 mM '[U-100% 15N]' $entity_AP5 2.5 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing 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_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.4 . pH pressure 1 . atm temperature 273 . K stop_ save_ save_H_exch_rate_list_1 _Saveframe_category H_exchange_rates _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _H_exchange_rate_units min-1 _Mol_system_component_name 'adenylate kinase' _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Atom_name _H_exchange_rate_value _H_exchange_rate_min_value _H_exchange_rate_max_value _H_exchange_rate_value_error 58 LEU H 0.0159 . . . stop_ save_