HEADER TRANSFERASE 30-NOV-20 7KW8 TITLE NMR STRUCTURE OF A TRNA 2'-PHOSPHOTRANSFERASE FROM RUNELLA TITLE 2 SLITHYFORMIS 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, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.ALPHONSE,S.DANTULURI,A.BANERJEE,S.SHUMAN,R.GHOSE REVDAT 3 15-MAY-24 7KW8 1 REMARK REVDAT 2 14-JUN-23 7KW8 1 REMARK REVDAT 1 13-OCT-21 7KW8 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 2997 RESTRAINTS, 2587 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 278 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 132 FROM HYDROGEN BONDS. REMARK 4 REMARK 4 7KW8 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_1000253231. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290.15; 290.15; 290.15; 290.15 REMARK 210 PH : 7; 7; 7; 7 REMARK 210 IONIC STRENGTH : 0; 0; 0; 0 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-13C; U-15N] TPT1, 20 REMARK 210 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-100% 2H] REMARK 210 EDTA, 5 % V/V [U-100% 2H] GLYCEROL, 0.5 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 0.04 % V/V SODIUM AZIDE, 50 UM DSS, 95% H2O/5% D2O; REMARK 210 360 UM [U-13C; U-15N] TPT1, 20 MM HEPES, 200 MM SODIUM CHLORIDE, REMARK 210 2 MM DTT, 2 MM [U-100% 2H] EDTA, 5 % V/V [U-100% 2H] GLYCEROL, REMARK 210 0.5 MM AEBSF PROTEASE INHIBITOR, 0.04 % V/V SODIUM AZIDE, 50 UM REMARK 210 DSS, 95% H2O/5% D2O; 300 UM [U-13C; U-15N] TPT1, 20 MM HEPES, REMARK 210 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-100% 2H] EDTA, 5 % V/V REMARK 210 [U-100% 2H] GLYCEROL, 1 MM AEBSF PROTEASE INHIBITOR, 0.05 % W/V REMARK 210 SODIUM AZIDE, 50 UM DSS, 95% H2O/5% D2O; 400 UM [U-13C; U-15N] REMARK 210 TPT1, 20 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-100% REMARK 210 2H] EDTA, 5 % V/V [U-100% 2H] GLYCEROL, 0.5 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 0.05 % W/V SODIUM AZIDE, 50 MM DSS, 100% D2O; 420 UM REMARK 210 [U-13C; U-15N] TPT1, 20 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM REMARK 210 DTT, 2 MM [U-100% 2H] EDTA, 5 % V/V [U-100% 2H] GLYCEROL, 0.5 MM REMARK 210 AEBSF PROTEASE INHIBITOR, 0.04 % W/V SODIUM AZIDE, 50 MM DSS, 95% REMARK 210 H2O/5% D2O; 380 UM [U-13C; U-15N] TPT1, 20 MM HEPES, 200 MM REMARK 210 SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-100% 2H] EDTA, 5 % V/V [U-100% REMARK 210 2H] GLYCEROL, 0.5 MM AEBSF PROTEASE INHIBITOR, 0.04 % W/V REMARK 210 SODIUM AZIDE, 50 MM DSS, 95% H2O/5% D2O; 400 UM [U-13C; U-15N] REMARK 210 TPT1, 20 MM HEPES, 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-100% REMARK 210 2H] EDTA, 5 % V/V [U-100% 2H] GLYCEROL, 0.5 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 0.04 % W/V SODIUM AZIDE, 50 MM DSS, 100% D2O; 400 UM REMARK 210 [U-2H; U-15N];[13CD1,1H3]ILE;[13CD1,1H3;13CD2,1H3]LEU;[13CG1,1H3; REMARK 210 13CG2,1H3]VAL;[13CE1,1H3]MET;[13CG2,1H3]THR TPT1, 20 MM HEPES, REMARK 210 200 MM SODIUM CHLORIDE, 2 MM DTT, 2 MM [U-100% 2H] EDTA, 5 % V/V REMARK 210 [U-100% 2H] GLYCEROL, 0.5 MM AEBSF PROTEASE INHIBITOR, 0.05 % W/ REMARK 210 V SODIUM AZIDE, 50 UM DSS, 100% D2O; 350 UM [U-2H; U-15N];[13CD1, REMARK 210 1H3]ILE;[13CD1,1H3;13CD2,1H3]LEU;[13CG1,1H3;13CG2,1H3]VAL;[13CE1, REMARK 210 1H3]MET;[13CG2,1H3]THR TPT1, 20 MM HEPES, 200 MM SODIUM CHLORIDE, REMARK 210 2 MM DTT, 2 MM [U-100% 2H] EDTA, 5 % V/V [U-100% 2H] GLYCEROL, REMARK 210 0.5 MM AEBSF PROTEASE INHIBITOR, 0.05 % W/V SODIUM AZIDE, 50 UM REMARK 210 DSS, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-13C METHYL NOESY; REMARK 210 1H-13C-13C-1H 4D NOESY; 3D HNCA; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 3D CCH-TOCSY; REMARK 210 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 12 PRO A 94 C - N - CA ANGL. DEV. = 9.5 DEGREES 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 HIS A 3 16.44 -162.82 REMARK 500 1 HIS A 17 -73.37 -110.69 REMARK 500 1 ASP A 27 -179.78 -69.92 REMARK 500 1 SER A 61 -71.99 -106.15 REMARK 500 1 LYS A 62 -79.49 55.72 REMARK 500 1 ASN A 77 -71.78 -88.37 REMARK 500 1 GLN A 78 -179.71 66.96 REMARK 500 1 SER A 81 31.27 -93.01 REMARK 500 1 GLU A 83 92.26 -67.17 REMARK 500 1 ASP A 85 90.37 40.10 REMARK 500 1 TYR A 88 -161.49 -125.60 REMARK 500 1 PRO A 94 -87.16 -32.01 REMARK 500 1 LYS A 116 -71.92 -138.63 REMARK 500 1 ARG A 119 -33.53 165.26 REMARK 500 1 HIS A 120 117.10 -162.90 REMARK 500 1 HIS A 121 86.49 72.31 REMARK 500 1 PHE A 170 143.97 -176.04 REMARK 500 2 SER A 2 -39.51 -145.27 REMARK 500 2 ARG A 16 -41.28 -130.14 REMARK 500 2 HIS A 17 -74.73 -103.76 REMARK 500 2 LYS A 44 40.63 -85.77 REMARK 500 2 SER A 61 77.86 -159.59 REMARK 500 2 ASP A 85 115.57 51.40 REMARK 500 2 PRO A 94 176.57 -53.55 REMARK 500 2 LYS A 115 -69.03 -155.42 REMARK 500 2 MET A 117 81.09 65.08 REMARK 500 2 PHE A 170 147.83 -176.28 REMARK 500 3 HIS A 17 -73.76 -111.72 REMARK 500 3 PHE A 71 13.52 56.84 REMARK 500 3 GLU A 83 70.40 62.88 REMARK 500 3 ASP A 85 23.46 49.05 REMARK 500 3 PRO A 94 157.40 -32.21 REMARK 500 3 LYS A 115 -81.58 -165.74 REMARK 500 3 LYS A 116 -62.13 63.74 REMARK 500 3 HIS A 120 -35.29 160.69 REMARK 500 3 PRO A 141 154.22 -49.53 REMARK 500 4 ARG A 16 -48.17 -133.80 REMARK 500 4 HIS A 17 -74.58 -104.15 REMARK 500 4 SER A 61 70.61 -158.74 REMARK 500 4 GLU A 83 79.17 62.44 REMARK 500 4 PRO A 94 -156.76 -69.70 REMARK 500 4 LYS A 111 -62.87 -96.16 REMARK 500 4 LYS A 115 128.50 -170.39 REMARK 500 4 LYS A 116 -61.87 -132.00 REMARK 500 4 MET A 117 88.34 -151.17 REMARK 500 5 HIS A 17 -73.79 -110.73 REMARK 500 5 LYS A 44 42.76 -75.60 REMARK 500 5 HIS A 46 -30.26 -142.05 REMARK 500 5 ASN A 60 -72.17 -104.83 REMARK 500 5 SER A 61 48.88 -106.23 REMARK 500 REMARK 500 THIS ENTRY HAS 205 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7KW9 RELATED DB: PDB REMARK 900 CONTAINTS THE SAME PROTEIN COMPLEXED WITH NAD+ REMARK 900 RELATED ID: 30819 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF A TRNA 2'-PHOSPHOTRANSFERASE FROM RUNELLA REMARK 900 SLITHYFORMIS DBREF 7KW8 A 1 178 PDB 7KW8 7KW8 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 HELIX 1 AA1 HIS A 3 LEU A 15 1 13 HELIX 2 AA2 ASN A 18 GLY A 23 5 6 HELIX 3 AA3 VAL A 34 LYS A 44 1 11 HELIX 4 AA4 SER A 49 ASN A 60 1 12 HELIX 5 AA5 ASN A 105 GLY A 113 1 9 HELIX 6 AA6 ASP A 127 MET A 136 1 10 HELIX 7 AA7 ALA A 148 GLY A 155 1 8 SHEET 1 AA1 3 ALA A 32 PRO A 33 0 SHEET 2 AA1 3 LYS A 73 ALA A 76 -1 O ILE A 74 N ALA A 32 SHEET 3 AA1 3 PHE A 65 PHE A 67 -1 N ALA A 66 O ARG A 75 SHEET 1 AA2 2 VAL A 96 ALA A 102 0 SHEET 2 AA2 2 PRO A 141 ASP A 147 -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 ILE A 168 N VAL A 122 SHEET 3 AA3 3 PHE A 158 LEU A 160 -1 N TYR A 159 O LEU A 167 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