HEADER LYASE 10-DEC-03 1RSQ TITLE STRUCTURE OF RAT LIVER THREONINE DEAMINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-SERINE DEHYDRATASE/L-THREONINE DEAMINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-SERINE DEHYDRATASE, L-SERINE DEAMINASE, SDH, L- COMPND 5 THREONINE DEHYDRATASE, L-THREONINE DEAMINASE, TDH; COMPND 6 EC: 4.3.1.19 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 STRAIN: WISTAR; SOURCE 5 TISSUE: LIVER KEYWDS AMINOTRANSFERASE, PROTEIN MODELLING, PYRIDOXAL-PHOSPHATE, KEYWDS 2 THREONINE DEAMINASE EXPDTA THEORETICAL MODEL AUTHOR M.SCARSELLI,G.PADULA,A.BERNINI,O.SPIGA,A.CIUTTI,N.NICCOLAI REVDAT 1 13-JAN-04 1RSQ 0 JRNL AUTH M.SCARSELLI,M.G.PADULA,A.BERNINI,O.SPIGA,A.CIUTTI, JRNL AUTH 2 R.LEONCINI,D.VANNONI,E.MARINELLO,N.NICCOLAI JRNL TITL STRUCTURE AND FUNCTION CORRELATIONS BETWEEN THE JRNL TITL 2 RAT LIVER THREONINE DEAMINASE AND AMINOTRANSFERASES JRNL REF BIOCHIM.BIOPHYS.ACTA V.1645 40 2003 JRNL REFN ASTM BBACAQ NE ISSN 0006-3002 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMOS 96 REMARK 3 AUTHORS : FUJINAGA,GROS,VAN GUNSTEREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PEPTIDE BOND BETWEEN RESIDUES REMARK 3 119 AND 120 OF CHAIN A IS 1.81 ANGSTROMS REMARK 4 REMARK 4 1RSQ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-DEC-2003. REMARK 100 THE RCSB ID CODE IS RCSB021015. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL 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 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 REMARK 500 CD1 LEU A 115 CG2 VAL A 123 1.64 REMARK 500 O ALA A 150 CD PRO A 152 1.74 REMARK 500 O ASN A 118 CB PRO A 120 1.88 REMARK 500 O LYS A 113 N LYS A 117 1.89 REMARK 500 O LYS A 113 CB LYS A 117 1.96 REMARK 500 CB ALA A 154 O ALA A 267 1.97 REMARK 500 O GLY A 153 N ALA A 267 2.00 REMARK 500 O ASN A 118 CD PRO A 120 2.02 REMARK 500 O ASN A 118 N PRO A 120 2.04 REMARK 500 CA ALA A 154 O ALA A 267 2.05 REMARK 500 CG LEU A 115 CG2 VAL A 123 2.10 REMARK 500 O ALA A 114 O ASN A 118 2.18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 149 C ALA A 150 N -0.227 REMARK 500 VAL A 175 C GLY A 176 N 0.146 REMARK 500 TRP A 177 NE1 TRP A 177 CE2 -0.177 REMARK 500 TRP A 177 CE2 TRP A 177 CZ2 0.110 REMARK 500 TRP A 177 CD2 TRP A 177 CE3 -0.123 REMARK 500 GLU A 178 N GLU A 178 CA 0.144 REMARK 500 TRP A 177 C GLU A 178 N -0.159 REMARK 500 PRO A 260 N PRO A 260 CA 0.142 REMARK 500 GLU A 259 C PRO A 260 N -0.144 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 SER A 149 CA - C - N ANGL. DEV. = 36.1 DEGREES REMARK 500 SER A 149 O - C - N ANGL. DEV. =-84.7 DEGREES REMARK 500 VAL A 175 CA - C - N ANGL. DEV. = 26.2 DEGREES REMARK 500 VAL A 175 O - C - N ANGL. DEV. =-71.9 DEGREES REMARK 500 GLY A 176 C - N - CA ANGL. DEV. =-37.2 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 VAL A 101 -141.16 173.37 REMARK 500 GLU A 174 -129.13 -38.56 REMARK 500 TRP A 177 -86.06 93.16 REMARK 500 CYS A 262 129.99 62.38 REMARK 500 VAL A 273 -69.28 134.70 REMARK 500 LEU A 308 -42.24 113.67 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 LYS A 13 VAL A 14 148.77 REMARK 500 VAL A 19 PHE A 20 139.49 REMARK 500 GLY A 48 CYS A 49 149.90 REMARK 500 GLY A 121 TRP A 122 -139.99 REMARK 500 VAL A 175 GLY A 176 126.65 REMARK 500 VAL A 258 GLU A 259 147.63 REMARK 500 PRO A 260 ALA A 261 65.51 REMARK 500 ALA A 261 CYS A 262 144.23 REMARK 500 GLN A 278 ALA A 279 -114.32 REMARK 500 CYS A 295 GLY A 296 -128.25 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 64-99 IN THE SEQUENCE DATABASE REFERENCE ARE REMARK 999 MISSING IN THE NATURAL VARIANT WHOSE SEQUENCE WAS USED REMARK 999 FOR THIS STRUCTURE. RESIDUES 11 AND 275 OF THE SEQUENCE REMARK 999 DATABASE REPRESENT NATURAL VARIATIONS IN THE SEQUENCE. DBREF 1RSQ A 1 319 UNP P09367 SDHL_RAT 8 362 SEQADV 1RSQ THR A 4 UNP P09367 PRO 11 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 VAL 64 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 VAL 65 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLN 66 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ILE 67 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 TRP 68 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLY 69 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 SER 70 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ARG 71 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 MET 72 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ARG 73 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLY 74 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ARG 75 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 SER 76 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 HIS 77 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 SER 78 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLY 79 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ASP 80 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLU 81 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLN 82 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 PRO 83 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 HIS 84 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 VAL 85 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ARG 86 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 SER 87 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 GLN 88 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ALA 89 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 LEU 90 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 LEU 91 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 PRO 92 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 ASP 93 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 THR 94 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 PRO 95 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 SER 96 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 PRO 97 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 LEU 98 SEE REMARK 999 SEQADV 1RSQ A UNP P09367 THR 99 SEE REMARK 999 SEQADV 1RSQ THR A 232 UNP P09367 PRO 275 SEE REMARK 999 SEQRES 1 A 319 VAL LYS THR THR LEU ARG ASP SER MET ALA LEU SER LYS SEQRES 2 A 319 VAL ALA GLY THR SER VAL PHE LEU LYS MET ASP SER SER SEQRES 3 A 319 GLN PRO SER GLY SER PHE LYS ILE ARG GLY ILE GLY HIS SEQRES 4 A 319 LEU CYS LYS MET LYS ALA LYS GLN GLY CYS LYS HIS PHE SEQRES 5 A 319 VAL CYS SER SER ALA GLY ASN ALA GLY MET ALA THR ALA SEQRES 6 A 319 TYR ALA ALA ARG ARG LEU GLY LEU PRO ALA THR ILE VAL SEQRES 7 A 319 VAL PRO SER THR THR PRO ALA LEU THR ILE GLU ARG LEU SEQRES 8 A 319 LYS ASN GLU GLY ALA THR VAL GLU VAL VAL GLY GLU MET SEQRES 9 A 319 LEU ASP GLU ALA ILE GLN LEU ALA LYS ALA LEU GLU LYS SEQRES 10 A 319 ASN ASN PRO GLY TRP VAL TYR ILE SER PRO PHE ASP ASP SEQRES 11 A 319 PRO LEU ILE TRP GLU GLY HIS THR SER LEU VAL LYS GLU SEQRES 12 A 319 LEU LYS GLU THR LEU SER ALA LYS PRO GLY ALA ILE VAL SEQRES 13 A 319 LEU SER VAL GLY GLY GLY GLY LEU LEU CYS GLY VAL VAL SEQRES 14 A 319 GLN GLY LEU ARG GLU VAL GLY TRP GLU ASP VAL PRO ILE SEQRES 15 A 319 ILE ALA MET GLU THR PHE GLY ALA HIS SER PHE HIS ALA SEQRES 16 A 319 ALA VAL LYS GLU GLY LYS LEU VAL THR LEU PRO LYS ILE SEQRES 17 A 319 THR SER VAL ALA LYS ALA LEU GLY VAL ASN THR VAL GLY SEQRES 18 A 319 ALA GLN THR LEU LYS LEU PHE TYR GLU HIS THR ILE PHE SEQRES 19 A 319 SER GLU VAL ILE SER ASP GLN GLU ALA VAL THR ALA ILE SEQRES 20 A 319 GLU LYS PHE VAL ASP ASP GLU LYS ILE LEU VAL GLU PRO SEQRES 21 A 319 ALA CYS GLY ALA ALA LEU ALA ALA VAL TYR SER GLY VAL SEQRES 22 A 319 VAL CYS ARG LEU GLN ALA GLU GLY ARG LEU GLN THR PRO SEQRES 23 A 319 LEU ALA SER LEU VAL VAL ILE VAL CYS GLY GLY SER ASN SEQRES 24 A 319 ILE SER LEU ALA GLN LEU GLN ALA LEU LYS ALA GLN LEU SEQRES 25 A 319 GLY LEU ASN GLU LEU LEU LYS HET PLP 321 16 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 COMPLEX FORMUL 2 PLP C8 H10 N O6 P HELIX 1 1 ASP A 7 VAL A 14 1 8 HELIX 2 2 MET A 23 SER A 26 5 4 HELIX 3 3 PHE A 32 ILE A 37 1 6 HELIX 4 4 HIS A 39 MET A 43 5 5 HELIX 5 5 GLY A 58 LEU A 71 1 14 HELIX 6 6 THR A 83 GLU A 94 1 12 HELIX 7 7 MET A 104 ASN A 118 1 15 HELIX 8 8 ASP A 129 LEU A 148 1 20 HELIX 9 9 GLY A 161 GLU A 174 1 14 HELIX 10 10 ALA A 190 GLU A 199 1 10 HELIX 11 11 GLY A 221 PHE A 228 1 8 HELIX 12 12 TYR A 229 HIS A 231 5 3 HELIX 13 13 ILE A 238 ALA A 243 1 6 HELIX 14 14 THR A 245 PHE A 250 1 6 HELIX 15 15 ALA A 279 THR A 285 1 7 HELIX 16 16 SER A 298 GLN A 306 1 9 SHEET 1 A 6 THR A 4 ARG A 6 0 SHEET 2 A 6 THR A 17 LEU A 21 -1 O PHE A 20 N LEU A 5 SHEET 3 A 6 ALA A 265 ALA A 268 1 O ALA A 268 N VAL A 19 SHEET 4 A 6 GLY A 153 VAL A 156 1 N GLY A 153 O ALA A 265 SHEET 5 A 6 ILE A 182 GLU A 186 1 O ILE A 182 N VAL A 156 SHEET 6 A 6 ILE A 233 VAL A 237 1 O ILE A 233 N ILE A 183 SHEET 1 B 4 ALA A 96 VAL A 98 0 SHEET 2 B 4 PRO A 74 ILE A 77 1 N THR A 76 O ALA A 96 SHEET 3 B 4 PHE A 52 SER A 55 1 N CYS A 54 O ILE A 77 SHEET 4 B 4 TRP A 122 VAL A 123 1 O TRP A 122 N VAL A 53 CISPEP 1 SER A 149 ALA A 150 0 -7.61 CRYST1 102.402 102.402 102.402 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 0.009765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009765 0.00000 MASTER 131 0 1 16 10 0 0 6 0 0 0 25 END