HEADER OXIDOREDUCTASE 22-MAY-02 1LUD TITLE SOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TITLE 2 TRIMETHOPRIM AND NADPH, 24 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 3 ORGANISM_TAXID: 1582; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: NF1; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMT702 KEYWDS DHFR, INHIBITOR-ENZYME COMPLEX, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR V.I.POLSHAKOV,E.G.SMIRNOV,B.BIRDSALL,G.KELLY,J.FEENEY REVDAT 3 28-DEC-16 1LUD 1 JRNL REMARK VERSN REVDAT 2 24-FEB-09 1LUD 1 VERSN REVDAT 1 18-DEC-02 1LUD 0 JRNL AUTH V.I.POLSHAKOV,E.G.SMIRNOV,B.BIRDSALL,G.KELLY,J.FEENEY JRNL TITL NMR-BASED SOLUTION STRUCTURE OF THE COMPLEX OF LACTOBACILLUS JRNL TITL 2 CASEI DIHYDROFOLATE REDUCTASE WITH TRIMETHOPRIM AND NADPH JRNL REF J.BIOMOL.NMR V. 24 67 2002 JRNL REFN ISSN 0925-2738 JRNL PMID 12449420 JRNL DOI 10.1023/A:1020659713373 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.I.POLSHAKOV,R.R.BIEKOFSKY,B.BIRDSALL,J.FEENEY REMARK 1 TITL TOWARDS UNDERSTANDING THE ORIGINS OF THE DIFFERENT REMARK 1 TITL 2 SPECIFICITIES OF BINDING THE REDUCED (NADPH) AND OXYDISED REMARK 1 TITL 3 (NADP+) FORMS OF NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE REMARK 1 TITL 4 COENZYME TO DIHYDROFOLATE REDUCTASE REMARK 1 REF J.MOL.STRUCT. V. 602 257 2002 REMARK 1 REFN ISSN 0022-2860 REMARK 1 DOI 10.1016/S0022-2860(01)00687-1 REMARK 1 REFERENCE 2 REMARK 1 AUTH V.I.POLSHAKOV,B.BIRDSALL,J.FEENEY REMARK 1 TITL CHARACTERIZATION OF RATES OF RING-FLIPPING IN TRIMETHOPRIM REMARK 1 TITL 2 IN ITS TERNARY COMPLEXES WITH LACTOBACILLUS CASEI REMARK 1 TITL 3 DIHYDROFOLATE REDUCTASE AND COENZYME ANALOGUES REMARK 1 REF BIOCHEMISTRY V. 38 15962 1999 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 10625463 REMARK 1 DOI 10.1021/BI9915263 REMARK 1 REFERENCE 3 REMARK 1 AUTH V.I.POLSHAKOV,B.BIRDSALL,T.A.FRENKIEL,A.R.GARGARO,J.FEENEY REMARK 1 TITL STRUCTURE AND DYNAMICS IN SOLUTION OF THE COMPLEX OF REMARK 1 TITL 2 LACTOBACILLUS CASEI DIHYDROFOLATE REDUCTASE WITH THE NEW REMARK 1 TITL 3 LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE REMARK 1 REF PROTEIN SCI. V. 8 467 1999 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 10091649 REMARK 1 DOI 10.1110/PS.8.3.467 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.R.GARGARO,A.SOTERIOU,T.A.FRENKIEL,C.J.BAUER,B.BIRDSALL, REMARK 1 AUTH 2 V.I.POLSHAKOV,I.L.BARSUKOV,G.C.K.ROBERTS,J.FEENEY REMARK 1 TITL THE SOLUTION STRUCTURE OF THE COMPLEX OF LACTOBACILLUS CASEI REMARK 1 TITL 2 DIHYDROFOLATE REDUCTASE WITH METHOTREXATE REMARK 1 REF J.MOL.BIOL. V. 277 119 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1997.1560 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 10 PS AT 1000K, 40 PS COOLING FROM 1000 REMARK 3 TO 0K, 1000 STEPS OF EM REMARK 4 REMARK 4 1LUD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016278. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3MM DHFR-15N/TMP/NADPH, 50 MM REMARK 210 PHOSPHATE BUFFER; 3 MM DHFR/TMP/ REMARK 210 NADPH, 50 MM PHOSPHATE BUFFER; REMARK 210 0.5MM DHFR-15N/TMP/NADPH, 50 MM REMARK 210 PHOSPHATE BUFFER, 5% DMPC/DHPC REMARK 210 (3:1); 0.25MM DHFR-15N/TMP/NADPH, REMARK 210 50 MM PHOSPHATE BUFFER, 5% C12E5/ REMARK 210 HEXANOL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; HNHA; REMARK 210 3D_15N-SEPARATED_ROESY; 2D_N15- REMARK 210 REJECTED_NOESY; 2D NOESY; DQF- REMARK 210 COSY; J-MODULATED N15, H1-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, NMRPIPE 1998-2001, CNS REMARK 210 0.9 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 32 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 O ALA A 2 H ILE A 96 1.56 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 ILE A 13 -67.44 -130.91 REMARK 500 1 PHE A 49 154.91 -48.56 REMARK 500 1 ASP A 78 108.70 -167.99 REMARK 500 1 ASP A 91 11.51 -141.31 REMARK 500 1 ASP A 111 -35.60 -131.36 REMARK 500 2 TRP A 21 -159.38 -113.84 REMARK 500 2 ASP A 78 106.80 -166.86 REMARK 500 2 GLU A 93 -159.84 -87.28 REMARK 500 3 ILE A 13 -63.32 -133.43 REMARK 500 3 TRP A 21 -157.51 -114.45 REMARK 500 3 PRO A 55 156.12 -48.69 REMARK 500 3 GLU A 56 23.10 49.64 REMARK 500 3 ASP A 78 109.86 -167.86 REMARK 500 3 ASP A 91 10.45 -143.10 REMARK 500 4 LEU A 19 154.36 -49.91 REMARK 500 4 PHE A 49 159.83 -44.64 REMARK 500 4 ASP A 78 113.33 -167.56 REMARK 500 4 ASP A 91 10.93 -141.17 REMARK 500 5 ILE A 13 -65.77 -122.33 REMARK 500 5 HIS A 18 -167.93 -56.67 REMARK 500 5 PHE A 49 159.90 -43.22 REMARK 500 5 ASP A 78 111.05 -166.08 REMARK 500 6 ILE A 13 -66.88 -131.29 REMARK 500 6 HIS A 18 -165.93 -56.28 REMARK 500 6 ASP A 78 114.19 -166.74 REMARK 500 6 PRO A 130 99.20 -54.03 REMARK 500 7 ILE A 13 -62.58 -135.70 REMARK 500 7 HIS A 18 -165.81 -58.18 REMARK 500 7 PHE A 49 150.59 -45.10 REMARK 500 7 ASP A 78 111.54 -167.19 REMARK 500 7 PRO A 130 96.58 -66.59 REMARK 500 8 ILE A 13 -66.74 -121.31 REMARK 500 8 ASP A 78 111.39 -168.75 REMARK 500 8 GLU A 93 -158.25 -90.67 REMARK 500 9 HIS A 18 -165.58 -56.66 REMARK 500 9 PHE A 49 161.88 -46.12 REMARK 500 9 ASP A 78 109.23 -166.04 REMARK 500 10 ILE A 13 -63.14 -129.71 REMARK 500 10 ASP A 78 114.18 -167.53 REMARK 500 10 PRO A 130 99.27 -58.79 REMARK 500 11 HIS A 18 -166.57 -57.68 REMARK 500 11 TRP A 21 -158.77 -113.23 REMARK 500 11 PHE A 49 154.77 -47.06 REMARK 500 11 ASP A 78 107.18 -168.78 REMARK 500 11 ASP A 91 10.82 -140.33 REMARK 500 12 ILE A 13 -67.30 -130.95 REMARK 500 12 LEU A 19 164.32 -48.93 REMARK 500 12 TRP A 21 -158.57 -112.98 REMARK 500 12 ASP A 78 108.13 -166.43 REMARK 500 13 HIS A 18 -171.62 -55.25 REMARK 500 REMARK 500 THIS ENTRY HAS 95 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 NDP A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRR A 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BZF RELATED DB: PDB REMARK 900 1BZF CONTAINS THE SAME PROTEIN COMPLEXED WITH THE NEW REMARK 900 LIPOPHILIC ANTIFOLATE DRUG TRIMETREXATE REMARK 900 RELATED ID: 1AO8 RELATED DB: PDB REMARK 900 1AO8 CONTAINS THE SAME PROTEIN COMPLEXED WITH METHOTREXATE REMARK 900 RELATED ID: 3DFR RELATED DB: PDB REMARK 900 3DFR CONTAINS CRYSTAL STRUCTURE OF THE SAME PROTEIN REMARK 900 COMPLEXED WITH NADPH AND METHOTREXATE DBREF 1LUD A 1 162 UNP P00381 DYR_LACCA 1 162 SEQRES 1 A 162 THR ALA PHE LEU TRP ALA GLN ASP ARG ASP GLY LEU ILE SEQRES 2 A 162 GLY LYS ASP GLY HIS LEU PRO TRP HIS LEU PRO ASP ASP SEQRES 3 A 162 LEU HIS TYR PHE ARG ALA GLN THR VAL GLY LYS ILE MET SEQRES 4 A 162 VAL VAL GLY ARG ARG THR TYR GLU SER PHE PRO LYS ARG SEQRES 5 A 162 PRO LEU PRO GLU ARG THR ASN VAL VAL LEU THR HIS GLN SEQRES 6 A 162 GLU ASP TYR GLN ALA GLN GLY ALA VAL VAL VAL HIS ASP SEQRES 7 A 162 VAL ALA ALA VAL PHE ALA TYR ALA LYS GLN HIS PRO ASP SEQRES 8 A 162 GLN GLU LEU VAL ILE ALA GLY GLY ALA GLN ILE PHE THR SEQRES 9 A 162 ALA PHE LYS ASP ASP VAL ASP THR LEU LEU VAL THR ARG SEQRES 10 A 162 LEU ALA GLY SER PHE GLU GLY ASP THR LYS MET ILE PRO SEQRES 11 A 162 LEU ASN TRP ASP ASP PHE THR LYS VAL SER SER ARG THR SEQRES 12 A 162 VAL GLU ASP THR ASN PRO ALA LEU THR HIS THR TYR GLU SEQRES 13 A 162 VAL TRP GLN LYS LYS ALA HET NDP A 168 74 HET TRR A 170 40 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM TRR 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 TRR C14 H19 N4 O3 1+ HELIX 1 1 LEU A 23 THR A 34 1 12 HELIX 2 2 ARG A 43 PHE A 49 1 7 HELIX 3 3 ASP A 78 HIS A 89 1 12 HELIX 4 4 GLY A 99 PHE A 106 1 8 HELIX 5 5 ASN A 132 ASP A 134 5 3 SHEET 1 A 8 VAL A 74 VAL A 76 0 SHEET 2 A 8 THR A 58 LEU A 62 1 N VAL A 61 O VAL A 76 SHEET 3 A 8 ILE A 38 GLY A 42 1 N MET A 39 O VAL A 60 SHEET 4 A 8 LEU A 94 GLY A 98 1 O VAL A 95 N VAL A 40 SHEET 5 A 8 ALA A 2 GLN A 7 1 N ALA A 2 O ILE A 96 SHEET 6 A 8 THR A 112 LEU A 118 1 O THR A 112 N PHE A 3 SHEET 7 A 8 HIS A 153 LYS A 160 -1 O TRP A 158 N LEU A 113 SHEET 8 A 8 PHE A 136 VAL A 144 -1 N ARG A 142 O TYR A 155 CISPEP 1 ARG A 52 PRO A 53 1 -0.88 CISPEP 2 GLY A 98 GLY A 99 1 0.96 CISPEP 3 ARG A 52 PRO A 53 2 -0.97 CISPEP 4 GLY A 98 GLY A 99 2 0.89 CISPEP 5 ARG A 52 PRO A 53 3 -0.44 CISPEP 6 GLY A 98 GLY A 99 3 1.04 CISPEP 7 ARG A 52 PRO A 53 4 -0.12 CISPEP 8 GLY A 98 GLY A 99 4 1.00 CISPEP 9 ARG A 52 PRO A 53 5 -0.88 CISPEP 10 GLY A 98 GLY A 99 5 1.00 CISPEP 11 ARG A 52 PRO A 53 6 0.01 CISPEP 12 GLY A 98 GLY A 99 6 1.00 CISPEP 13 ARG A 52 PRO A 53 7 0.50 CISPEP 14 GLY A 98 GLY A 99 7 1.38 CISPEP 15 ARG A 52 PRO A 53 8 -0.22 CISPEP 16 GLY A 98 GLY A 99 8 0.91 CISPEP 17 ARG A 52 PRO A 53 9 -0.28 CISPEP 18 GLY A 98 GLY A 99 9 0.91 CISPEP 19 ARG A 52 PRO A 53 10 -0.67 CISPEP 20 GLY A 98 GLY A 99 10 1.34 CISPEP 21 ARG A 52 PRO A 53 11 -1.04 CISPEP 22 GLY A 98 GLY A 99 11 0.81 CISPEP 23 ARG A 52 PRO A 53 12 -0.32 CISPEP 24 GLY A 98 GLY A 99 12 0.92 CISPEP 25 ARG A 52 PRO A 53 13 -0.22 CISPEP 26 GLY A 98 GLY A 99 13 1.06 CISPEP 27 ARG A 52 PRO A 53 14 -0.71 CISPEP 28 GLY A 98 GLY A 99 14 1.10 CISPEP 29 ARG A 52 PRO A 53 15 -0.67 CISPEP 30 GLY A 98 GLY A 99 15 1.03 CISPEP 31 ARG A 52 PRO A 53 16 -0.84 CISPEP 32 GLY A 98 GLY A 99 16 0.90 CISPEP 33 ARG A 52 PRO A 53 17 -0.94 CISPEP 34 GLY A 98 GLY A 99 17 1.23 CISPEP 35 ARG A 52 PRO A 53 18 -0.48 CISPEP 36 GLY A 98 GLY A 99 18 1.09 CISPEP 37 ARG A 52 PRO A 53 19 -0.98 CISPEP 38 GLY A 98 GLY A 99 19 1.23 CISPEP 39 ARG A 52 PRO A 53 20 0.07 CISPEP 40 GLY A 98 GLY A 99 20 1.13 CISPEP 41 ARG A 52 PRO A 53 21 -0.57 CISPEP 42 GLY A 98 GLY A 99 21 1.16 CISPEP 43 ARG A 52 PRO A 53 22 -0.02 CISPEP 44 GLY A 98 GLY A 99 22 1.29 CISPEP 45 ARG A 52 PRO A 53 23 0.06 CISPEP 46 GLY A 98 GLY A 99 23 1.03 CISPEP 47 ARG A 52 PRO A 53 24 0.15 CISPEP 48 GLY A 98 GLY A 99 24 1.05 SITE 1 AC1 20 TRP A 5 ALA A 6 ILE A 13 GLY A 14 SITE 2 AC1 20 LYS A 15 GLY A 17 GLY A 42 ARG A 43 SITE 3 AC1 20 ARG A 44 THR A 45 LEU A 62 THR A 63 SITE 4 AC1 20 HIS A 64 GLN A 65 ALA A 97 GLY A 99 SITE 5 AC1 20 ALA A 100 GLN A 101 ILE A 102 TRR A 170 SITE 1 AC2 13 LEU A 4 TRP A 5 ALA A 6 GLY A 17 SITE 2 AC2 13 LEU A 19 ASP A 26 LEU A 27 PHE A 30 SITE 3 AC2 13 PHE A 49 PRO A 50 ALA A 97 THR A 116 SITE 4 AC2 13 NDP A 168 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