HEADER TRANSFERASE 30-NOV-20 7KW9 TITLE NMR STRUCTURE OF A TRNA 2'-PHOSPHOTRANSFERASE FROM RUNELLA TITLE 2 SLITHYFORMIS IN COMPLEX WITH NAD+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA 2'-PHOSPHOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TPT1; COMPND 5 EC: 2.7.1.160; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUNELLA SLITHYFORMIS; SOURCE 3 ORGANISM_TAXID: 106; SOURCE 4 ATCC: 49304; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRNA 2'-PHOSPHOTRANSFERASE NAD+, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.ALPHONSE,S.DANTULURI,A.BANERJEE,S.SHUMAN,R.GHOSE REVDAT 3 15-MAY-24 7KW9 1 REMARK REVDAT 2 14-JUN-23 7KW9 1 REMARK REVDAT 1 13-OCT-21 7KW9 0 JRNL AUTH S.ALPHONSE,A.BANERJEE,S.DANTULURI,S.SHUMAN,R.GHOSE JRNL TITL NMR SOLUTION STRUCTURES OF RUNELLA SLITHYFORMIS RNA JRNL TITL 2 2'-PHOSPHOTRANSFERASE TPT1 PROVIDE INSIGHTS INTO NAD+ JRNL TITL 3 BINDING AND SPECIFICITY. JRNL REF NUCLEIC ACIDS RES. V. 49 9607 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33880546 JRNL DOI 10.1093/NAR/GKAB241 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.52 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 3773 RESTRAINTS, 3368 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 269 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 136 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 7KW9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253230. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290.15; 290.15 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 0; 0 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 600 UM [U-13C; U-15N] TPT1, 2.4 REMARK 210 MM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 MM HEPES, 200 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 2 MM [U-2H] EDTA, 5 % V/V [U-2H] GLYCEROL, 1 REMARK 210 MM AEBSF PROTEASE INHIBITOR, 0.04 % W/V SODIUM AZIDE, 50 UM DSS, REMARK 210 95% H2O/5% D2O; 280 UM [U-13C; U-15N] TPT1, 1.12 MM NICOTINAMIDE- REMARK 210 ADENINE-DINUCLEOTIDE, 20 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM REMARK 210 DTT, 2 MM [U-2H] EDTA, 5 % V/V [U-2H] GLYCEROL, 1 MM AEBSF REMARK 210 PROTEASE INHIBITOR, 0.04 % W/V SODIUM AZIDE, 50 UM DSS, 95% H2O/ REMARK 210 5% D2O; 325 UM [U-13C; U-15N] TPT1, 1.3 MM NICOTINAMIDE-ADENINE- REMARK 210 DINUCLEOTIDE, 20 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 REMARK 210 MM [U-2H] EDTA, 5 % V/V [U-2H] GLYCEROL, 1 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 0.04 % W/V SODIUM AZIDE, 50 UM DSS, 100% D2O; 300 UM REMARK 210 [U-13C; U-15N] TPT1, 1.2 MM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, REMARK 210 20 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-2H] EDTA, REMARK 210 5 % V/V [U-2H] GLYCEROL, 1 MM AEBSF PROTEASE INHIBITOR, 0.04 % W/ REMARK 210 V SODIUM AZIDE, 50 UM DSS, 100% D2O; 500 UM [U-13C; U-15N; U-2H] REMARK 210 TPT1, 2 MM NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 MM HEPES, 200 REMARK 210 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-2H] EDTA, 5 % V/V [U-2H] REMARK 210 GLYCEROL, 1 MM AEBSF PROTEASE INHIBITOR, 0.04 % W/V SODIUM AZIDE, REMARK 210 50 UM DSS, 95% H2O/5% D2O; 400 UM [U-13C; U-15N] TPT1, 1.6 MM REMARK 210 NICOTINAMIDE-ADENINE-DINUCLEOTIDE, 20 MM HEPES, 200 MM SODIUM REMARK 210 CHLORIDE, 2 MM DTT, 2 MM [U-2H] EDTA, 5 % V/V [U-2H] GLYCEROL, 1 REMARK 210 MM AEBSF PROTEASE INHIBITOR, 0.04 % W/V SODIUM AZIDE, 50 UM DSS, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HN(CA)CO; 3D HNCA; REMARK 210 3D HN(CO)CA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 C(CO)NH; 3D H(CCO)NH; 3D CCH- REMARK 210 TOCSY; 3D HCCH-TOCSY; 2D 1H-1H REMARK 210 NOESY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 METHYL; 4D 1H-13C-13C-1H NOESY REMARK 210 METHYL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 10.3 REVISION REMARK 210 2019.220.13.40, TOPSPIN 3.5P15, REMARK 210 NMRVIEW, ARIA 2.3.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU A 83 HD1 HIS A 120 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 2 78.47 63.75 REMARK 500 1 HIS A 17 -53.69 -128.46 REMARK 500 1 ALA A 20 -8.24 -57.75 REMARK 500 1 ASN A 60 -12.70 -44.87 REMARK 500 1 GLN A 78 178.41 165.26 REMARK 500 1 SER A 81 81.76 -68.51 REMARK 500 1 GLU A 83 -75.09 -103.93 REMARK 500 1 VAL A 84 -81.19 -137.37 REMARK 500 1 ASP A 85 82.00 177.93 REMARK 500 1 VAL A 92 105.88 -54.91 REMARK 500 1 HIS A 99 119.59 -162.56 REMARK 500 1 LYS A 116 102.31 -59.28 REMARK 500 1 HIS A 120 89.35 60.78 REMARK 500 2 ASN A 18 51.40 -157.24 REMARK 500 2 ALA A 20 -7.98 -57.09 REMARK 500 2 LYS A 63 55.22 73.26 REMARK 500 2 PHE A 71 32.21 72.82 REMARK 500 2 GLU A 83 5.69 -158.15 REMARK 500 2 LYS A 115 -65.34 -131.00 REMARK 500 2 MET A 117 -50.63 -175.68 REMARK 500 2 SER A 118 12.97 -144.29 REMARK 500 2 GLN A 126 -38.95 -154.92 REMARK 500 2 PHE A 170 134.13 -174.73 REMARK 500 3 ALA A 20 -9.60 -58.63 REMARK 500 3 HIS A 46 -61.15 -99.48 REMARK 500 3 ASN A 60 -14.06 -46.96 REMARK 500 3 GLN A 78 61.36 -154.15 REMARK 500 3 SER A 81 70.88 52.75 REMARK 500 3 VAL A 84 -41.87 -139.50 REMARK 500 3 ASP A 85 86.07 153.99 REMARK 500 3 GLU A 89 -47.82 -160.01 REMARK 500 3 LYS A 90 93.17 75.29 REMARK 500 3 LYS A 115 -59.63 -124.82 REMARK 500 3 LYS A 116 -71.38 -147.35 REMARK 500 3 SER A 118 67.88 73.71 REMARK 500 4 ASN A 18 53.80 -149.40 REMARK 500 4 ALA A 20 -7.71 -56.44 REMARK 500 4 ASN A 60 -12.85 -44.73 REMARK 500 4 SER A 61 -12.16 -45.46 REMARK 500 4 GLN A 78 -65.77 -145.55 REMARK 500 4 GLU A 83 -3.66 89.66 REMARK 500 4 TYR A 88 90.73 44.23 REMARK 500 4 LYS A 115 -46.59 -134.48 REMARK 500 4 LYS A 116 128.62 -170.83 REMARK 500 4 SER A 118 -62.42 -161.76 REMARK 500 4 HIS A 120 36.57 -82.89 REMARK 500 4 PHE A 170 116.93 -166.50 REMARK 500 5 ASN A 18 51.51 -151.90 REMARK 500 5 ALA A 20 -7.89 -57.81 REMARK 500 5 ASN A 60 -12.86 -44.54 REMARK 500 REMARK 500 THIS ENTRY HAS 253 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KW8 RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN IN APO FORM REMARK 900 RELATED ID: 30820 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF A TRNA 2'-PHOSPHOTRANSFERASE FROM RUNELLA REMARK 900 SLITHYFORMIS IN COMPLEX WITH NAD+ DBREF 7KW9 A 1 178 PDB 7KW9 7KW9 1 178 SEQRES 1 A 178 GLY SER HIS MET VAL LYS VAL SER LYS PHE LEU SER LEU SEQRES 2 A 178 VAL LEU ARG HIS ASN PRO ALA LEU ILE GLY LEU ASP LEU SEQRES 3 A 178 ASP ALA ASN GLY TRP ALA PRO VAL LYS GLU LEU LEU ALA SEQRES 4 A 178 LYS MET LYS ALA LYS GLY HIS GLY ILE SER MET GLU GLU SEQRES 5 A 178 LEU LYS HIS ILE VAL GLU THR ASN SER LYS LYS ARG PHE SEQRES 6 A 178 ALA PHE SER GLU ASN PHE GLU LYS ILE ARG ALA ASN GLN SEQRES 7 A 178 GLY HIS SER VAL GLU VAL ASP LEU GLY TYR GLU LYS GLN SEQRES 8 A 178 VAL PRO PRO ALA VAL LEU PHE HIS GLY THR ALA GLU LYS SEQRES 9 A 178 ASN PHE ASP LEU ILE LEU LYS ASP GLY ILE LYS LYS MET SEQRES 10 A 178 SER ARG HIS HIS VAL HIS LEU SER GLN ASP ILE THR THR SEQRES 11 A 178 ALA ARG LYS VAL GLY MET ARG HIS GLY LYS PRO VAL VAL SEQRES 12 A 178 LEU SER VAL ASP ALA LYS GLY MET ALA ASP GLY GLY PHE SEQRES 13 A 178 ASP PHE TYR LEU SER ASN ASN GLY VAL TRP LEU ILE ASP SEQRES 14 A 178 PHE VAL PRO ALA GLU PHE ILE LYS VAL HET NAD A 201 70 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 2 NAD C21 H27 N7 O14 P2 HELIX 1 AA1 HIS A 3 LEU A 15 1 13 HELIX 2 AA2 VAL A 34 LYS A 44 1 11 HELIX 3 AA3 SER A 49 THR A 59 1 11 HELIX 4 AA4 ASN A 60 LYS A 63 5 4 HELIX 5 AA5 GLU A 103 ASP A 112 1 10 HELIX 6 AA6 ASP A 127 MET A 136 1 10 HELIX 7 AA7 ASP A 147 GLY A 154 1 8 SHEET 1 AA1 3 ALA A 32 PRO A 33 0 SHEET 2 AA1 3 LYS A 73 ARG A 75 -1 O ILE A 74 N ALA A 32 SHEET 3 AA1 3 ALA A 66 PHE A 67 -1 N ALA A 66 O ARG A 75 SHEET 1 AA2 2 GLY A 100 ALA A 102 0 SHEET 2 AA2 2 PRO A 141 VAL A 143 -1 O VAL A 142 N THR A 101 SHEET 1 AA3 3 VAL A 122 LEU A 124 0 SHEET 2 AA3 3 TRP A 166 ILE A 168 -1 O TRP A 166 N LEU A 124 SHEET 3 AA3 3 TYR A 159 LEU A 160 -1 N TYR A 159 O LEU A 167 SHEET 1 AA4 2 SER A 145 VAL A 146 0 SHEET 2 AA4 2 ILE A 176 LYS A 177 -1 O LYS A 177 N SER A 145 SITE 1 AC1 16 HIS A 99 THR A 101 ASN A 105 LEU A 108 SITE 2 AC1 16 ILE A 109 ASP A 112 GLY A 113 ILE A 114 SITE 3 AC1 16 MET A 117 HIS A 123 LEU A 124 SER A 125 SITE 4 AC1 16 GLN A 126 VAL A 134 ASN A 163 VAL A 165 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 2834 2835 2836 2837 2856 CONECT 2835 2834 CONECT 2836 2834 CONECT 2837 2834 2838 CONECT 2838 2837 2839 2878 2879 CONECT 2839 2838 2840 2841 2880 CONECT 2840 2839 2845 CONECT 2841 2839 2842 2843 2881 CONECT 2842 2841 2882 CONECT 2843 2841 2844 2845 2883 CONECT 2844 2843 2884 CONECT 2845 2840 2843 2846 2885 CONECT 2846 2845 2847 2855 CONECT 2847 2846 2848 2886 CONECT 2848 2847 2849 CONECT 2849 2848 2850 2855 CONECT 2850 2849 2851 2852 CONECT 2851 2850 2887 2888 CONECT 2852 2850 2853 CONECT 2853 2852 2854 2889 CONECT 2854 2853 2855 CONECT 2855 2846 2849 2854 CONECT 2856 2834 2857 CONECT 2857 2856 2858 2859 2860 CONECT 2858 2857 CONECT 2859 2857 CONECT 2860 2857 2861 CONECT 2861 2860 2862 2890 2891 CONECT 2862 2861 2863 2864 2892 CONECT 2863 2862 2868 CONECT 2864 2862 2865 2866 2893 CONECT 2865 2864 2894 CONECT 2866 2864 2867 2868 2895 CONECT 2867 2866 2896 CONECT 2868 2863 2866 2869 2897 CONECT 2869 2868 2870 2877 CONECT 2870 2869 2871 2898 CONECT 2871 2870 2872 2875 CONECT 2872 2871 2873 2874 CONECT 2873 2872 CONECT 2874 2872 2899 2900 CONECT 2875 2871 2876 2901 CONECT 2876 2875 2877 2902 CONECT 2877 2869 2876 2903 CONECT 2878 2838 CONECT 2879 2838 CONECT 2880 2839 CONECT 2881 2841 CONECT 2882 2842 CONECT 2883 2843 CONECT 2884 2844 CONECT 2885 2845 CONECT 2886 2847 CONECT 2887 2851 CONECT 2888 2851 CONECT 2889 2853 CONECT 2890 2861 CONECT 2891 2861 CONECT 2892 2862 CONECT 2893 2864 CONECT 2894 2865 CONECT 2895 2866 CONECT 2896 2867 CONECT 2897 2868 CONECT 2898 2870 CONECT 2899 2874 CONECT 2900 2874 CONECT 2901 2875 CONECT 2902 2876 CONECT 2903 2877 MASTER 192 0 1 7 10 0 4 6 1441 1 70 14 END