HEADER HYDROLASE 16-APR-08 2K31 TITLE SOLUTION STRUCTURE OF CGMP-BINDING GAF DOMAIN OF PHOSPHODIESTERASE 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHODIESTERASE 5A, CGMP-SPECIFIC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CGMP-BINDING GAF DOMAIN (UNP RESIDUES 154-320); COMPND 5 EC: 3.1.4.35; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 GENE: PDE5A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)STAR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PRUNH KEYWDS CYCLIC NUCLEOTIDE PHOSPHODIESTERASE, PDE5, GAF DOMAIN, CGMP, KEYWDS 2 HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.C.HEIKAUS,J.R.STOUT,M.R.SEKHARAN,C.M.EAKIN,P.RAJAGOPAL,P.S.BRZOVIC, AUTHOR 2 J.A.BEAVO,R.E.KLEVIT REVDAT 6 08-MAY-24 2K31 1 REMARK REVDAT 5 20-OCT-21 2K31 1 REMARK SEQADV REVDAT 4 19-FEB-20 2K31 1 REMARK SEQADV REVDAT 3 24-FEB-09 2K31 1 VERSN REVDAT 2 26-AUG-08 2K31 1 JRNL REVDAT 1 03-JUN-08 2K31 0 JRNL AUTH C.C.HEIKAUS,J.R.STOUT,M.R.SEKHARAN,C.M.EAKIN,P.RAJAGOPAL, JRNL AUTH 2 P.S.BRZOVIC,J.A.BEAVO,R.E.KLEVIT JRNL TITL SOLUTION STRUCTURE OF THE CGMP BINDING GAF DOMAIN FROM JRNL TITL 2 PHOSPHODIESTERASE 5: INSIGHTS INTO NUCLEOTIDE SELECTIVITY, JRNL TITL 3 DIMERIZATION, AND CGMP-DEPENDENT CONFORMATIONAL CHANGE. JRNL REF J.BIOL.CHEM. V. 283 22749 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18534985 JRNL DOI 10.1074/JBC.M801577200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CYANA 2.0 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K31 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000100612. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.5 - 1.2 MM GUANOSINE-3',5' REMARK 210 -MONOPHOSPHATE, 0.5 - 1.2 MM REMARK 210 MPDE5_GAFA, 150 MM SODIUM REMARK 210 CHLORIDE, 1 MM PMSF, 1-5 MM DTT, REMARK 210 0.1 MM EDTA, 25 MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.5 - REMARK 210 1.2 MM GUANOSINE-3',5'- REMARK 210 MONOPHOSPHATE, 0.5 - 1.2 MM [U- REMARK 210 100% 15N] MPDE5_GAFA, 150 MM REMARK 210 SODIUM CHLORIDE, 1 MM PMSF, 1-5 REMARK 210 MM DTT, 0.1 MM EDTA, 25 MM REMARK 210 SODIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 0.5 - 1.2 MM GUANOSINE-3',5' REMARK 210 -MONOPHOSPHATE, 0.5 - 1.2 MM [U- REMARK 210 100% 13C; U-100% 15N; 80% 2H] REMARK 210 MPDE5_GAFA, 150 MM SODIUM REMARK 210 CHLORIDE, 1 MM PMSF, 1-5 MM DTT, REMARK 210 0.1 MM EDTA, 25 MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.5 - REMARK 210 1.2 MM GUANOSINE-3',5'- REMARK 210 MONOPHOSPHATE, 0.5 - 1.2 MM [U- REMARK 210 100% 13C; U-100% 15N] MPDE5_GAFA, REMARK 210 150 MM SODIUM CHLORIDE, 1 MM REMARK 210 PMSF, 1-5 MM DTT, 0.1 MM EDTA, REMARK 210 25 MM SODIUM PHOSPHATE, 90% H2O/ REMARK 210 10% D2O; 0.5 - 1.2 MM GUANOSINE- REMARK 210 3',5'-MONOPHOSPHATE, 0.5 - 1.2 REMARK 210 MM [U-100% 15N] MPDE5_GAFA, 150 REMARK 210 MM SODIUM CHLORIDE, 1 MM PMSF, 1- REMARK 210 5 MM DTT, 0.1 MM EDTA, 25 MM REMARK 210 SODIUM PHOSPHATE, 100% D2O; 0.5 - REMARK 210 1.2 MM GUANOSINE-3',5'- REMARK 210 MONOPHOSPHATE, 0.5 - 1.2 MM [U- REMARK 210 100% 13C; U-100% 15N] MPDE5_GAFA, REMARK 210 150 MM SODIUM CHLORIDE, 1 MM REMARK 210 PMSF, 1-5 MM DTT, 0.1 MM EDTA, REMARK 210 25 MM SODIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D HNCO; 3D HNCA; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HCCH-COSY; 3D HN(COCA)CB; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, NMRDRAW, NMRVIEW, REMARK 210 MODELFREE, TALOS 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 THE LOWEST REMARK 210 ENERGY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 153 REMARK 465 VAL A 303 REMARK 465 LEU A 304 REMARK 465 HIS A 305 REMARK 465 ASN A 306 REMARK 465 ALA A 307 REMARK 465 GLN A 308 REMARK 465 LEU A 309 REMARK 465 TYR A 310 REMARK 465 GLU A 311 REMARK 465 THR A 312 REMARK 465 SER A 313 REMARK 465 LEU A 314 REMARK 465 LEU A 315 REMARK 465 GLU A 316 REMARK 465 ASN A 317 REMARK 465 LYS A 318 REMARK 465 ARG A 319 REMARK 465 ASN A 320 REMARK 465 LEU A 321 REMARK 465 GLU A 322 REMARK 465 HIS A 323 REMARK 465 HIS A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 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: 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 171 98.89 51.42 REMARK 500 1 LYS A 186 65.70 61.78 REMARK 500 1 ASP A 196 98.94 55.25 REMARK 500 1 ASN A 209 110.29 60.14 REMARK 500 1 LYS A 217 -57.26 -121.41 REMARK 500 1 ASP A 234 102.89 -175.16 REMARK 500 1 ARG A 240 70.56 -119.70 REMARK 500 1 ARG A 265 7.08 134.72 REMARK 500 1 VAL A 269 -38.29 -131.76 REMARK 500 2 SER A 171 100.53 56.96 REMARK 500 2 ASP A 173 -60.40 -103.64 REMARK 500 2 LYS A 186 62.64 62.11 REMARK 500 2 ASP A 196 91.80 55.47 REMARK 500 2 ASN A 209 -64.82 67.98 REMARK 500 2 CYS A 210 154.38 61.82 REMARK 500 2 LYS A 217 -57.15 -122.91 REMARK 500 2 ASP A 234 105.12 -167.04 REMARK 500 2 ARG A 265 -9.22 135.31 REMARK 500 2 VAL A 268 146.11 66.97 REMARK 500 2 VAL A 269 -36.10 -134.63 REMARK 500 3 THR A 156 47.07 -97.19 REMARK 500 3 SER A 171 103.53 56.70 REMARK 500 3 LYS A 186 66.03 61.54 REMARK 500 3 ASP A 196 90.51 46.32 REMARK 500 3 ASN A 209 114.76 61.82 REMARK 500 3 LYS A 217 -52.38 -125.47 REMARK 500 3 ARG A 240 72.48 -115.96 REMARK 500 3 ARG A 265 7.50 132.36 REMARK 500 3 VAL A 269 -37.78 -130.48 REMARK 500 4 VAL A 155 -44.52 -139.44 REMARK 500 4 SER A 171 101.74 56.12 REMARK 500 4 LYS A 186 66.24 60.89 REMARK 500 4 ASP A 196 98.46 62.86 REMARK 500 4 ASN A 209 119.91 62.96 REMARK 500 4 LYS A 217 -54.67 -123.33 REMARK 500 4 ASP A 234 106.85 -168.28 REMARK 500 4 ARG A 265 7.36 133.74 REMARK 500 4 VAL A 269 -35.44 -138.69 REMARK 500 4 THR A 284 -173.86 61.28 REMARK 500 5 SER A 171 102.77 57.63 REMARK 500 5 ASP A 196 71.81 55.43 REMARK 500 5 ASN A 209 -69.86 66.72 REMARK 500 5 CYS A 210 150.62 61.98 REMARK 500 5 ARG A 240 74.06 -107.43 REMARK 500 5 ARG A 265 6.58 133.74 REMARK 500 5 LYS A 278 -74.79 -96.65 REMARK 500 5 SER A 279 -46.30 -143.39 REMARK 500 5 THR A 284 -60.14 -93.95 REMARK 500 6 SER A 171 96.84 56.36 REMARK 500 6 LYS A 186 65.62 61.85 REMARK 500 REMARK 500 THIS ENTRY HAS 188 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 35G A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15734 RELATED DB: BMRB DBREF 2K31 A 154 320 UNP Q0VBW0 Q0VBW0_MOUSE 154 320 SEQADV 2K31 MET A 153 UNP Q0VBW0 INITIATING METHIONINE SEQADV 2K31 GLU A 295 UNP Q0VBW0 ALA 295 ENGINEERED MUTATION SEQADV 2K31 GLU A 302 UNP Q0VBW0 ILE 302 ENGINEERED MUTATION SEQADV 2K31 LEU A 321 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 GLU A 322 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 HIS A 323 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 HIS A 324 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 HIS A 325 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 HIS A 326 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 HIS A 327 UNP Q0VBW0 EXPRESSION TAG SEQADV 2K31 HIS A 328 UNP Q0VBW0 EXPRESSION TAG SEQRES 1 A 176 MET ASP VAL THR ALA LEU CYS HIS LYS ILE PHE LEU HIS SEQRES 2 A 176 ILE HIS GLY LEU ILE SER ALA ASP ARG TYR SER LEU PHE SEQRES 3 A 176 LEU VAL CYS GLU ASP SER SER LYS ASP LYS PHE LEU ILE SEQRES 4 A 176 SER ARG LEU PHE ASP VAL ALA GLU GLY SER THR LEU GLU SEQRES 5 A 176 GLU ALA SER ASN ASN CYS ILE ARG LEU GLU TRP ASN LYS SEQRES 6 A 176 GLY ILE VAL GLY HIS VAL ALA ALA PHE GLY GLU PRO LEU SEQRES 7 A 176 ASN ILE LYS ASP ALA TYR GLU ASP PRO ARG PHE ASN ALA SEQRES 8 A 176 GLU VAL ASP GLN ILE THR GLY TYR LYS THR GLN SER ILE SEQRES 9 A 176 LEU CYS MET PRO ILE LYS ASN HIS ARG GLU GLU VAL VAL SEQRES 10 A 176 GLY VAL ALA GLN ALA ILE ASN LYS LYS SER GLY ASN GLY SEQRES 11 A 176 GLY THR PHE THR GLU LYS ASP GLU LYS ASP PHE ALA GLU SEQRES 12 A 176 TYR LEU ALA PHE CYS GLY GLU VAL LEU HIS ASN ALA GLN SEQRES 13 A 176 LEU TYR GLU THR SER LEU LEU GLU ASN LYS ARG ASN LEU SEQRES 14 A 176 GLU HIS HIS HIS HIS HIS HIS HET 35G A 1 34 HETNAM 35G GUANOSINE-3',5'-MONOPHOSPHATE FORMUL 2 35G C10 H12 N5 O7 P HELIX 1 1 ALA A 157 HIS A 167 1 11 HELIX 2 2 GLU A 204 SER A 207 1 4 HELIX 3 3 GLY A 218 GLY A 227 1 10 HELIX 4 4 GLU A 244 GLY A 250 1 7 HELIX 5 5 THR A 286 GLY A 301 1 16 SHEET 1 A 6 ARG A 212 GLU A 214 0 SHEET 2 A 6 ASP A 187 LEU A 194 -1 N LEU A 190 O LEU A 213 SHEET 3 A 6 ARG A 174 ASP A 183 -1 N CYS A 181 O PHE A 189 SHEET 4 A 6 GLU A 267 ILE A 275 -1 O VAL A 271 N PHE A 178 SHEET 5 A 6 ILE A 256 ASN A 263 -1 N ASN A 263 O GLU A 267 SHEET 6 A 6 LEU A 230 ILE A 232 -1 N LEU A 230 O CYS A 258 SITE 1 AC1 9 ARG A 174 TYR A 175 SER A 176 PHE A 178 SITE 2 AC1 9 PHE A 195 LEU A 213 ILE A 219 ALA A 235 SITE 3 AC1 9 TYR A 236 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