HEADER OXIDOREDUCTASE 13-MAY-01 1IN9 TITLE HOMOLOGY-BASED THEORETICAL MOLECULAR MODEL OF HUMAN TITLE 2 TRYPTOPHAN HYDROXYLASE REGULATORY, CATALYTIC AND TITLE 3 TETRAMERIZATION DOMAINS CAVEAT 1IN9 THERE ARE SOME CHIRALITY ERRORS IN THE STRUCTURE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHAN HYDROXYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.16.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN KEYWDS OXIDOREDUCTASE EXPDTA THEORETICAL MODEL AUTHOR G.C.T.JIANG,G.J.YOHRLING IV,J.D.SCHMITT,K.E.VRANA REVDAT 2 01-APR-03 1IN9 1 JRNL REVDAT 1 23-MAY-01 1IN9 0 JRNL AUTH G.C.JIANG,G.J.YOHRLING 4TH.,J.D.SCHMITT,K.E.VRANA JRNL TITL IDENTIFICATION OF SUBSTRATE ORIENTING AND JRNL TITL 2 PHOSPHORYLATION SITES WITHIN TRYPTOPHAN JRNL TITL 3 HYDROXYLASE USING HOMOLOGY-BASED MOLECULAR JRNL TITL 4 MODELING. JRNL REF J.MOL.BIOL. V. 302 1005 2000 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IN9 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-2001. REMARK 100 THE RCSB ID CODE IS RCSB013427. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THE THREE-DIMENSIONAL MODEL OF HUMAN TRYPTOPHAN REMARK 220 HYDROXYLASE WAS GENERATED USING THE MULTIPLE SEQUENCE REMARK 220 ALIGNMENT MODELING APPROACH IN THE "COMPOSER" MODULE OF REMARK 220 SYBYL 6.5 (TRIPOS INC., ST. LOUIS, MO). THE REMARK 220 EXPERIMENTALLY-SOLVED STRUCTURES OF PHENYLALANINE REMARK 220 HYDROXYLASE (1PHZ AND 1PAH) (KOBE ET AL., 1999; REMARK 220 ERLANDSEN ET AL., 1997) AND TYROSINE HYDROXYLASE (1TOH) REMARK 220 (GOODWILL ET AL., 1997) WERE USED AS TEMPLATE MOLECULES REMARK 220 IN A MODULAR METHOD TO PROVIDE THE MOST COMPLETE MODEL. REMARK 220 INITIALLY, HUMAN TPH WAS PREDICTED BASED ON 1PHZ, 1PAH REMARK 220 AND 1TOH. THIS YIELDED AN INITIAL STRUCTURE WITH GAPS AT REMARK 220 POSITIONS 1, 65-66, 100-101, AND 411-444. THE GAPS THAT REMARK 220 RESULTED WITHIN THE PROTEIN (RESIDUES 65-66, AND 100- REMARK 220 101) WERE BRIDGED USING THE "LOOP SEARCH" FUNCTIONALITY REMARK 220 IN THE SYBYL BIOPOLYMER MODULE. BEFORE THE LOOP SEARCH, REMARK 220 EACH GAP WAS ENLARGED BY THE REMOVAL OF TWO AMINO ACIDS REMARK 220 FLANKING THE GAP. LOOP CANDIDATES WERE VISUALLY REMARK 220 EVALUATED AND CHOSEN ON THE BASIS OF COMPLEMENTARITY TO REMARK 220 THE EXISTING STRUCTURE. IN ORDER TO PROVIDE A COMPLETE REMARK 220 MODEL, HUMAN TPH WAS SEPARATELY PREDICTED BASED SOLELY REMARK 220 ON 1TOH AND THE CARBOXY TERMINUS OF THE RESULTING REMARK 220 STRUCTURE (RESIDUES 411-444) WAS THEN MERGED WITH ITS REMARK 220 RESPECTIVE CONTINUOUS, BUT TRUNCATED TPH MODEL BASED ON REMARK 220 1PHZ, 1PAH, AND 1TOH. THE RESULTING FULL LENGTH HUMAN REMARK 220 TPH MODEL (MISSING ONLY THE INITIATOR METHIONINE REMARK 220 RESIDUE) WAS SUBJECTED TO FURTHER REFINEMENT USING THE REMARK 220 PROGRAM PROCHECK TO ASSESS PROGRESS (LASKOWSKI ET AL., REMARK 220 1993). FIRST, POLAR HYDROGEN ATOMS WERE ADDED, THEN REMARK 220 PROLINE AND SIDECHAIN CONFORMATIONS WERE FIXED AND REMARK 220 RELIEVED OF BAD CONTACTS. NEXT, THE PEPTIDE BACKBONE WAS REMARK 220 CONSTRAINED AND THE MODEL WAS SUBJECTED TO CONVERGENT REMARK 220 MINIMIZATION, WITHOUT ELECTROSTATICS, IN THE TRIPOS REMARK 220 FORCEFIELD (CLARK ET AL., 1989). ALL THE REMAINING REMARK 220 VALENCIES WERE HYDROGEN-FILLED AND THE MODEL WAS AGAIN REMARK 220 MINIMIZED TO CONVERGENCE. BACKBONE CONSTRAINTS WERE THEN REMARK 220 REMOVED AND THE MODEL WAS MINIMIZED TO A HIGH LEVEL OF REMARK 220 CONVERGENCE (GRADIENT 0.005 KCAL/MOL). KOLLMAN CHARGES REMARK 220 (WEINER ET AL., 1984) WERE THEN ADDED FOLLOWED BY FIVE REMARK 220 CYCLES OF MINIMIZATION, DURING WHICH TIME THE DIELECTRIC REMARK 220 CONSTANT WAS GRADUALLY DECREASED FROM E = 80 TO E = 20. REMARK 220 THE FINAL MINIMIZATION STEP WAS CARRIED OUT TO REMARK 220 CONVERGENCE AT A HIGH LEVEL (GRADIENT 0.005 KCAL/MOL). REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 63 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 64 CB CG1 CG2 REMARK 470 ASP A 65 CB CG OD1 OD2 REMARK 470 CYS A 66 CB SG REMARK 470 ASP A 67 CB CG OD1 OD2 REMARK 470 ILE A 68 CB CG1 CG2 CD1 REMARK 470 ASN A 69 CB CG OD1 ND2 REMARK 470 ARG A 70 CB CG CD NE CZ NH1 NH2 REMARK 470 GLU A 71 CB CG CD OE1 OE2 REMARK 470 GLN A 72 CB CG CD OE1 NE2 REMARK 470 LYS A 98 CB CG CD CE NZ REMARK 470 GLU A 99 CB CG CD OE1 OE2 REMARK 470 ASP A 100 CB CG OD1 OD2 REMARK 470 MET A 102 CB CG SD CE REMARK 470 GLU A 103 CB CG CD OE1 OE2 REMARK 470 ARG A 121 CB CG CD NE CZ NH1 NH2 REMARK 470 VAL A 122 CB CG1 CG2 REMARK 470 LEU A 123 CB CG CD1 CD2 REMARK 470 TYR A 125 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 125 OH 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 239 CG - CD - NE ANGL. DEV. = 14.0 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 GLU A 3 -44.35 138.90 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 127 GLU A 128 147.52 DBREF 1IN9 A 2 444 GB 37955 CAA37018 2 444 SEQADV 1IN9 GLU A 97 GB 37955 LEU 97 CONFLICT SEQRES 1 A 443 ILE GLU ASP ASN LYS GLU ASN LYS ASP HIS SER LEU GLU SEQRES 2 A 443 ARG GLY ARG ALA SER LEU ILE PHE SER LEU LYS ASN GLU SEQRES 3 A 443 VAL GLY GLY LEU ILE LYS ALA LEU LYS ILE PHE GLN GLU SEQRES 4 A 443 LYS HIS VAL ASN LEU LEU HIS ILE GLU SER ARG LYS SER SEQRES 5 A 443 LYS ARG ARG ASN SER GLU PHE GLU ILE PHE VAL ASP CYS SEQRES 6 A 443 ASP ILE ASN ARG GLU GLN LEU ASN ASP ILE PHE HIS LEU SEQRES 7 A 443 LEU LYS SER HIS THR ASN VAL LEU SER VAL ASN LEU PRO SEQRES 8 A 443 ASP ASN PHE THR GLU LYS GLU ASP GLY MET GLU THR VAL SEQRES 9 A 443 PRO TRP PHE PRO LYS LYS ILE SER ASP LEU ASP HIS CYS SEQRES 10 A 443 ALA ASN ARG VAL LEU MET TYR GLY SER GLU LEU ASP ALA SEQRES 11 A 443 ASP HIS PRO GLY PHE LYS ASP ASN VAL TYR ARG LYS ARG SEQRES 12 A 443 ARG LYS TYR PHE ALA ASP LEU ALA MET ASN TYR LYS HIS SEQRES 13 A 443 GLY ASP PRO ILE PRO LYS VAL GLU PHE THR GLU GLU GLU SEQRES 14 A 443 ILE LYS THR TRP GLY THR VAL PHE GLN GLU LEU ASN LYS SEQRES 15 A 443 LEU TYR PRO THR HIS ALA CYS ARG GLU TYR LEU LYS ASN SEQRES 16 A 443 LEU PRO LEU LEU SER LYS TYR CYS GLY TYR ARG GLU ASP SEQRES 17 A 443 ASN ILE PRO GLN LEU GLU ASP VAL SER ASN PHE LEU LYS SEQRES 18 A 443 GLU ARG THR GLY PHE SER ILE ARG PRO VAL ALA GLY TYR SEQRES 19 A 443 LEU SER PRO ARG ASP PHE LEU SER GLY LEU ALA PHE ARG SEQRES 20 A 443 VAL PHE HIS CYS THR GLN TYR VAL ARG HIS SER SER ASP SEQRES 21 A 443 PRO PHE TYR THR PRO GLU PRO ASP THR CYS HIS GLU LEU SEQRES 22 A 443 LEU GLY HIS VAL PRO LEU LEU ALA GLU PRO SER PHE ALA SEQRES 23 A 443 GLN PHE SER GLN GLU ILE GLY LEU ALA SER LEU GLY ALA SEQRES 24 A 443 SER GLU GLU ALA VAL GLN LYS LEU ALA THR CYS TYR PHE SEQRES 25 A 443 PHE THR VAL GLU PHE GLY LEU CYS LYS GLN ASP GLY GLN SEQRES 26 A 443 LEU ARG VAL PHE GLY ALA GLY LEU LEU SER SER ILE SER SEQRES 27 A 443 GLU LEU LYS HIS ALA LEU SER GLY HIS ALA LYS VAL LYS SEQRES 28 A 443 PRO PHE ASP PRO LYS ILE THR CYS LYS GLN GLU CYS LEU SEQRES 29 A 443 ILE THR THR PHE GLN ASP VAL TYR PHE VAL SER GLU SER SEQRES 30 A 443 PHE GLU ASP ALA LYS GLU LYS MET ARG GLU PHE THR LYS SEQRES 31 A 443 THR ILE LYS ARG PRO PHE GLY VAL LYS TYR ASN PRO TYR SEQRES 32 A 443 THR ARG SER ILE GLN ILE LEU LYS ASP THR LYS SER ILE SEQRES 33 A 443 THR SER ALA MET ASN GLU LEU GLN HIS ASP LEU ASP VAL SEQRES 34 A 443 VAL SER ASP ALA LEU ALA LYS VAL SER ARG LYS PRO SER SEQRES 35 A 443 ILE HELIX 1 1 GLY A 29 LYS A 41 1 13 HELIX 2 2 CYS A 66 GLU A 71 1 6 HELIX 3 3 ASP A 75 VAL A 86 1 12 HELIX 4 4 GLU A 97 MET A 102 1 6 HELIX 5 5 LYS A 111 LEU A 115 5 5 HELIX 6 6 MET A 124 GLU A 128 5 5 HELIX 7 7 ASP A 138 TYR A 155 1 18 HELIX 8 8 THR A 167 TYR A 185 1 19 HELIX 9 9 PRO A 186 HIS A 188 5 3 HELIX 10 10 CYS A 190 CYS A 204 1 15 HELIX 11 11 GLN A 213 GLY A 226 1 14 HELIX 12 12 SER A 237 PHE A 247 1 11 HELIX 13 13 ASP A 269 HIS A 277 1 9 HELIX 14 14 HIS A 277 ALA A 282 1 6 HELIX 15 15 GLU A 283 LEU A 298 1 16 HELIX 16 16 SER A 301 THR A 315 1 15 HELIX 17 17 GLY A 333 SER A 336 5 4 HELIX 18 18 SER A 337 LEU A 345 1 9 HELIX 19 19 ASP A 355 LYS A 361 1 7 HELIX 20 20 SER A 378 ILE A 393 1 16 HELIX 21 21 ASP A 413 LYS A 441 1 29 HELIX 22 22 PRO A 442 ILE A 444 5 3 SHEET 1 A 3 PHE A 22 LYS A 25 0 SHEET 2 A 3 GLU A 59 VAL A 64 -1 N PHE A 60 O LEU A 24 SHEET 3 A 3 ILE A 48 LYS A 52 -1 O GLU A 49 N PHE A 63 SHEET 1 B 2 ASN A 94 PHE A 95 0 SHEET 2 B 2 VAL A 105 PRO A 106 1 O VAL A 105 N PHE A 95 SHEET 1 C 2 SER A 228 PRO A 231 0 SHEET 2 C 2 VAL A 249 CYS A 252 1 N PHE A 250 O SER A 228 SHEET 1 D 4 GLN A 326 VAL A 329 0 SHEET 2 D 4 LEU A 320 GLN A 323 -1 N CYS A 321 O ARG A 328 SHEET 3 D 4 VAL A 372 SER A 376 1 O PHE A 374 N LEU A 320 SHEET 4 D 4 LYS A 350 PRO A 353 1 O LYS A 350 N TYR A 373 SHEET 1 E 2 TYR A 401 ASN A 402 0 SHEET 2 E 2 SER A 407 ILE A 408 -1 O SER A 407 N ASN A 402 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 MASTER 130 0 0 22 13 0 0 6 0 0 0 35 END