HEADER OXIDOREDUCTASE(CHOH(D)-NAD+(A)) 10-NOV-92 1BMD 1BMD 2 COMPND MALATE DEHYDROGENASE (E.C.1.1.1.37) (BACTERIAL) COMPLEXED 1BMD 3 COMPND 2 WITH NADH 1BMD 4 SOURCE (THERMUS FLAVUS, STRAIN AT-62) 1BMD 5 AUTHOR C.A.KELLY,J.J.BIRKTOFT 1BMD 6 REVDAT 1 31-JUL-94 1BMD 0 1BMD 7 JRNL AUTH C.A.KELLY,M.NISHIYAMA,Y.OHNISHI,T.BEPPU, 1BMD 8 JRNL AUTH 2 J.J.BIRKTOFT 1BMD 9 JRNL TITL DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED 1BMD 10 JRNL TITL 2 IN THE 1.9 ANGSTROMS CRYSTAL STRUCTURE OF MALATE 1BMD 11 JRNL TITL 3 DEHYDROGENASE FROM THE THERMOPHILIC BACTERIUM 1BMD 12 JRNL TITL 4 THERMUS FLAVUS 1BMD 13 JRNL REF BIOCHEMISTRY V. 32 3913 1993 1BMD 14 JRNL REFN ASTM BICHAW US ISSN 0006-2960 0033 1BMD 15 REMARK 1 1BMD 16 REMARK 1 REFERENCE 1 1BMD 17 REMARK 1 AUTH C.A.KELLY,S.SARFATY,M.NISHIYAMA,T.BEPPU, 1BMD 18 REMARK 1 AUTH 2 J.J.BIRKTOFT 1BMD 19 REMARK 1 TITL PRELIMINARY X-RAY DIFFRACTION ANALYSIS OF A 1BMD 20 REMARK 1 TITL 2 CRYSTALLIZABLE MUTANT OF MALATE DEHYDROGENASE 1BMD 21 REMARK 1 TITL 3 FROM THE THERMOPHILE THERMUS FLAVUS 1BMD 22 REMARK 1 REF J.MOL.BIOL. V. 221 383 1991 1BMD 23 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1BMD 24 REMARK 1 REFERENCE 2 1BMD 25 REMARK 1 AUTH J.J.BIRKTOFT,G.RHODES,L.J.BANASZAK 1BMD 26 REMARK 1 TITL REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE 1BMD 27 REMARK 1 TITL 2 DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION 1BMD 28 REMARK 1 REF BIOCHEMISTRY V. 28 6065 1989 1BMD 29 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 0033 1BMD 30 REMARK 1 REFERENCE 3 1BMD 31 REMARK 1 AUTH M.NISHIYAMA,N.MATSUBARA,K.YAMAMOTO,S.IIJIMA, 1BMD 32 REMARK 1 AUTH 2 T.UOZUMI,T.BEPPU 1BMD 33 REMARK 1 TITL NUCLEOTIDE SEQUENCE OF THE MALATE DEHYDROGENASE 1BMD 34 REMARK 1 TITL 2 GENE OF THERMUS FLAVUS AND ITS MUTATION DIRECTING 1BMD 35 REMARK 1 TITL 3 AN INCREASE IN ENZYME ACTIVITY 1BMD 36 REMARK 1 REF J.BIOL.CHEM. V. 261 14178 1986 1BMD 37 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 0071 1BMD 38 REMARK 1 REFERENCE 4 1BMD 39 REMARK 1 AUTH J.J.BIRKTOFT,L.J.BANASZAK 1BMD 40 REMARK 1 TITL THE PRESENCE OF A HISTIDINE-ASPARTIC ACID PAIR IN 1BMD 41 REMARK 1 TITL 2 THE ACTIVE SITE OF 2-HYDROXYACID DEHYDROGENASES 1BMD 42 REMARK 1 REF J.BIOL.CHEM. V. 258 472 1983 1BMD 43 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 0071 1BMD 44 REMARK 1 REFERENCE 5 1BMD 45 REMARK 1 AUTH L.J.BANASZAK,R.A.BRADSHAW 1BMD 46 REMARK 1 TITL MALATE DEHYDROGENASES 1BMD 47 REMARK 1 REF ENZYME V. 11 369 1975 1BMD 48 REMARK 1 REFN ASTM ENZYBT SW ISSN 0013-9432 0818 1BMD 49 REMARK 2 1BMD 50 REMARK 2 RESOLUTION. 1.9 ANGSTROMS. 1BMD 51 REMARK 3 1BMD 52 REMARK 3 REFINEMENT. 1BMD 53 REMARK 3 PROGRAM 1 X-PLOR 1BMD 54 REMARK 3 AUTHORS 1 BRUNGER 1BMD 55 REMARK 3 PROGRAM 2 TNT 1BMD 56 REMARK 3 AUTHORS 2 TRONRUD,TEN EYCK,MATTHEWS 1BMD 57 REMARK 3 R VALUE 0.154 1BMD 58 REMARK 3 RMSD BOND DISTANCES 0.016 ANGSTROMS 1BMD 59 REMARK 3 RMSD BOND ANGLES 2.85 DEGREES 1BMD 60 REMARK 3 1BMD 61 REMARK 3 NUMBER OF PROTEIN ATOMS 4990 1BMD 62 REMARK 3 NUMBER OF SOLVENT ATOMS 288 1BMD 63 REMARK 4 1BMD 64 REMARK 4 RESIDUES GLU A 27, GLU B 27, AND ASP B 122 WERE FOUND TO 1BMD 65 REMARK 4 OCCUPY CLEARLY DEFINABLE MULTIPLE CONFORMATIONS WHOSE 1BMD 66 REMARK 4 COORDINATES ARE INCLUDED IN THIS DATA SET. THE 1BMD 67 REMARK 4 NICOTINAMIDE RING OF NADH AND THE SIDE CHAINS OF THE 1BMD 68 REMARK 4 FOLLOWING RESIDUES ARE MORE DISORDERED THAN THE REST: 1BMD 69 REMARK 4 GLN 14, ARG 91, LYS 92, GLU 96, ARG 97, ARG 98, ARG 178, 1BMD 70 REMARK 4 AND GLU 306. 1BMD 71 REMARK 5 1BMD 72 REMARK 5 THE NUMBERING SYSTEM IS THE SAME AS THAT USED FOR THE 1BMD 73 REMARK 5 CYTOPLASMIC MALATE DEHYDROGENASE STRUCTURE. THE DELETION 1BMD 74 REMARK 5 REGIONS IN TMDH, 201 - 204, 213, AND 276, LEAD TO 1BMD 75 REMARK 5 DISCONTINUITIES IN THE TMDH NUMBERING. HOWEVER, THERE ARE 1BMD 76 REMARK 5 NO BREAKS IN THE PEPTIDE CHAIN. 1BMD 77 REMARK 6 1BMD 78 REMARK 6 THE ASYMMETRIC UNIT CONTAINS TWO SUBUNITS WHICH HAVE BEEN 1BMD 79 REMARK 6 ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. THEY ARE RELATED 1BMD 80 REMARK 6 BY A NON-CRYSTALLOGRAPHIC SYMMETRY AXIS WITH A ROTATION 1BMD 81 REMARK 6 ANGLE OF 180.0 DEGREES. THE TRANSFORMATION PRESENTED ON 1BMD 82 REMARK 6 *MTRIX* RECORDS BELOW YIELDS OPTIMAL SUPERPOSITION OF 1BMD 83 REMARK 6 SUBUNIT A UPON SUBUNIT B BASED UPON ALL ALPHA CARBON ATOMS. 1BMD 84 REMARK 7 1BMD 85 REMARK 7 SEQUENCE ADVISORY NOTICE: 1BMD 86 REMARK 7 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. 1BMD 87 REMARK 7 1BMD 88 REMARK 7 SWISS-PROT ENTRY NAME: MDH_THEFL 1BMD 89 REMARK 7 1BMD 90 REMARK 7 SWISS-PROT RESIDUE PDB SEQRES 1BMD 91 REMARK 7 NAME NUMBER NAME CHAIN SEQ/INSERT CODE 1BMD 92 REMARK 7 LYS 75 ASP A 74 1BMD 93 REMARK 7 LYS 75 ASP B 74 1BMD 94 SEQRES 1 A 327 MET LYS ALA PRO VAL ARG VAL ALA VAL THR GLY ALA ALA 1BMD 95 SEQRES 2 A 327 GLY GLN ILE GLY TYR SER LEU LEU PHE ARG ILE ALA ALA 1BMD 96 SEQRES 3 A 327 GLY GLU MET LEU GLY LYS ASP GLN PRO VAL ILE LEU GLN 1BMD 97 SEQRES 4 A 327 LEU LEU GLU ILE PRO GLN ALA MET LYS ALA LEU GLU GLY 1BMD 98 SEQRES 5 A 327 VAL VAL MET GLU LEU GLU ASP CYS ALA PHE PRO LEU LEU 1BMD 99 SEQRES 6 A 327 ALA GLY LEU GLU ALA THR ASP ASP PRO ASP VAL ALA PHE 1BMD 100 SEQRES 7 A 327 LYS ASP ALA ASP TYR ALA LEU LEU VAL GLY ALA ALA PRO 1BMD 101 SEQRES 8 A 327 ARG LYS ALA GLY MET GLU ARG ARG ASP LEU LEU GLN VAL 1BMD 102 SEQRES 9 A 327 ASN GLY LYS ILE PHE THR GLU GLN GLY ARG ALA LEU ALA 1BMD 103 SEQRES 10 A 327 GLU VAL ALA LYS LYS ASP VAL LYS VAL LEU VAL VAL GLY 1BMD 104 SEQRES 11 A 327 ASN PRO ALA ASN THR ASN ALA LEU ILE ALA TYR LYS ASN 1BMD 105 SEQRES 12 A 327 ALA PRO GLY LEU ASN PRO ARG ASN PHE THR ALA MET THR 1BMD 106 SEQRES 13 A 327 ARG LEU ASP HIS ASN ARG ALA LYS ALA GLN LEU ALA LYS 1BMD 107 SEQRES 14 A 327 LYS THR GLY THR GLY VAL ASP ARG ILE ARG ARG MET THR 1BMD 108 SEQRES 15 A 327 VAL TRP GLY ASN HIS SER SER THR MET PHE PRO ASP LEU 1BMD 109 SEQRES 16 A 327 PHE HIS ALA GLU VAL ASP GLY ARG PRO ALA LEU GLU LEU 1BMD 110 SEQRES 17 A 327 VAL ASP MET GLU TRP TYR GLU LYS VAL PHE ILE PRO THR 1BMD 111 SEQRES 18 A 327 VAL ALA GLN ARG GLY ALA ALA ILE ILE GLN ALA ARG GLY 1BMD 112 SEQRES 19 A 327 ALA SER SER ALA ALA SER ALA ALA ASN ALA ALA ILE GLU 1BMD 113 SEQRES 20 A 327 HIS ILE ARG ASP TRP ALA LEU GLY THR PRO GLU GLY ASP 1BMD 114 SEQRES 21 A 327 TRP VAL SER MET ALA VAL PRO SER GLN GLY GLU TYR GLY 1BMD 115 SEQRES 22 A 327 ILE PRO GLU GLY ILE VAL TYR SER PHE PRO VAL THR ALA 1BMD 116 SEQRES 23 A 327 LYS ASP GLY ALA TYR ARG VAL VAL GLU GLY LEU GLU ILE 1BMD 117 SEQRES 24 A 327 ASN GLU PHE ALA ARG LYS ARG MET GLU ILE THR ALA GLN 1BMD 118 SEQRES 25 A 327 GLU LEU LEU ASP GLU MET GLU GLN VAL LYS ALA LEU GLY 1BMD 119 SEQRES 26 A 327 LEU ILE 1BMD 120 SEQRES 1 B 327 MET LYS ALA PRO VAL ARG VAL ALA VAL THR GLY ALA ALA 1BMD 121 SEQRES 2 B 327 GLY GLN ILE GLY TYR SER LEU LEU PHE ARG ILE ALA ALA 1BMD 122 SEQRES 3 B 327 GLY GLU MET LEU GLY LYS ASP GLN PRO VAL ILE LEU GLN 1BMD 123 SEQRES 4 B 327 LEU LEU GLU ILE PRO GLN ALA MET LYS ALA LEU GLU GLY 1BMD 124 SEQRES 5 B 327 VAL VAL MET GLU LEU GLU ASP CYS ALA PHE PRO LEU LEU 1BMD 125 SEQRES 6 B 327 ALA GLY LEU GLU ALA THR ASP ASP PRO ASP VAL ALA PHE 1BMD 126 SEQRES 7 B 327 LYS ASP ALA ASP TYR ALA LEU LEU VAL GLY ALA ALA PRO 1BMD 127 SEQRES 8 B 327 ARG LYS ALA GLY MET GLU ARG ARG ASP LEU LEU GLN VAL 1BMD 128 SEQRES 9 B 327 ASN GLY LYS ILE PHE THR GLU GLN GLY ARG ALA LEU ALA 1BMD 129 SEQRES 10 B 327 GLU VAL ALA LYS LYS ASP VAL LYS VAL LEU VAL VAL GLY 1BMD 130 SEQRES 11 B 327 ASN PRO ALA ASN THR ASN ALA LEU ILE ALA TYR LYS ASN 1BMD 131 SEQRES 12 B 327 ALA PRO GLY LEU ASN PRO ARG ASN PHE THR ALA MET THR 1BMD 132 SEQRES 13 B 327 ARG LEU ASP HIS ASN ARG ALA LYS ALA GLN LEU ALA LYS 1BMD 133 SEQRES 14 B 327 LYS THR GLY THR GLY VAL ASP ARG ILE ARG ARG MET THR 1BMD 134 SEQRES 15 B 327 VAL TRP GLY ASN HIS SER SER THR MET PHE PRO ASP LEU 1BMD 135 SEQRES 16 B 327 PHE HIS ALA GLU VAL ASP GLY ARG PRO ALA LEU GLU LEU 1BMD 136 SEQRES 17 B 327 VAL ASP MET GLU TRP TYR GLU LYS VAL PHE ILE PRO THR 1BMD 137 SEQRES 18 B 327 VAL ALA GLN ARG GLY ALA ALA ILE ILE GLN ALA ARG GLY 1BMD 138 SEQRES 19 B 327 ALA SER SER ALA ALA SER ALA ALA ASN ALA ALA ILE GLU 1BMD 139 SEQRES 20 B 327 HIS ILE ARG ASP TRP ALA LEU GLY THR PRO GLU GLY ASP 1BMD 140 SEQRES 21 B 327 TRP VAL SER MET ALA VAL PRO SER GLN GLY GLU TYR GLY 1BMD 141 SEQRES 22 B 327 ILE PRO GLU GLY ILE VAL TYR SER PHE PRO VAL THR ALA 1BMD 142 SEQRES 23 B 327 LYS ASP GLY ALA TYR ARG VAL VAL GLU GLY LEU GLU ILE 1BMD 143 SEQRES 24 B 327 ASN GLU PHE ALA ARG LYS ARG MET GLU ILE THR ALA GLN 1BMD 144 SEQRES 25 B 327 GLU LEU LEU ASP GLU MET GLU GLN VAL LYS ALA LEU GLY 1BMD 145 SEQRES 26 B 327 LEU ILE 1BMD 146 FTNOTE 1 1BMD 147 FTNOTE 1 SIDE CHAINS HAVE BEEN MODELED IN TWO ALTERNATE 1BMD 148 FTNOTE 1 CONFORMATIONS AND ASSIGNED ALTERNATE LOCATION INDICATORS 1BMD 149 FTNOTE 1 *1* AND *2*. 1BMD 150 FTNOTE 2 1BMD 151 FTNOTE 2 RESIDUES PRO A 131 AND PRO B 131 ARE CIS PROLINES. 1BMD 152 HET NAD A 334 44 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 1BMD 153 HET NAD B 334 44 NICOTINAMIDE-ADENINE-DINUCLEOTIDE 1BMD 154 FORMUL 3 NAD 2(C21 H28 N7 O14 P2) 1BMD 155 FORMUL 4 HOH *288(H2 O1) 1BMD 156 HELIX 1 BA GLN A 14 ALA A 24 1 1BMD 157 HELIX 2 CA PRO A 43 GLU A 57 1 1BMD 158 HELIX 3 CPA PRO A 73 ALA A 76 1 1BMD 159 HELIX 4 DEA ARG A 97 VAL A 118 1 1BMD 160 HELIX 5 1FA ALA A 132 LYS A 141 1 1BMD 161 HELIX 6 2FA ARG A 156 THR A 170 1 1BMD 162 HELIX 7 GPA ALA A 208 VAL A 212 1 1BMD 163 HELIX 8 1GA MET A 215 ALA A 227 1 1BMD 164 HELIX 9 2GA ARG A 229 ARG A 237 1 1BMD 165 HELIX 10 3GA ALA A 242 ALA A 257 1 1BMD 166 HELIX 11 HA GLU A 306 ALA A 328 1 1BMD 167 HELIX 12 BB GLN B 14 ALA B 24 1 1BMD 168 HELIX 13 CB PRO B 43 GLU B 57 1 1BMD 169 HELIX 14 CPB PRO B 73 ALA B 76 1 1BMD 170 HELIX 15 DEB ARG B 97 VAL B 118 1 1BMD 171 HELIX 16 1FB ALA B 132 LYS B 141 1 1BMD 172 HELIX 17 2FB ARG B 156 THR B 170 1 1BMD 173 HELIX 18 GPB ALA B 208 VAL B 212 1 1BMD 174 HELIX 19 1GB MET B 215 ALA B 227 1 1BMD 175 HELIX 20 2GB ARG B 229 ARG B 237 1 1BMD 176 HELIX 21 3GB ALA B 242 LEU B 258 1 1BMD 177 HELIX 22 HB GLU B 306 ALA B 328 1 1BMD 178 SHEET 1 S1A 6 LEU A 64 THR A 70 0 1BMD 179 SHEET 2 S1A 6 VAL A 35 LEU A 40 1 1BMD 180 SHEET 3 S1A 6 VAL A 4 THR A 9 1 1BMD 181 SHEET 4 S1A 6 TYR A 82 LEU A 85 1 1BMD 182 SHEET 5 S1A 6 LYS A 124 VAL A 127 1 1BMD 183 SHEET 6 S1A 6 PHE A 151 ALA A 153 1 1BMD 184 SHEET 1 S2A 3 ILE A 177 TRP A 183 0 1BMD 185 SHEET 2 S2A 3 PHE A 191 VAL A 199 -1 1BMD 186 SHEET 3 S2A 3 ARG A 206 PRO A 207 -1 1BMD 187 SHEET 1 S3A 3 VAL A 266 PRO A 271 0 1BMD 188 SHEET 2 S3A 3 VAL A 284 LYS A 292 -1 1BMD 189 SHEET 3 S3A 3 ALA A 295 VAL A 298 -1 1BMD 190 SHEET 1 S1B 6 LEU B 64 THR B 70 0 1BMD 191 SHEET 2 S1B 6 VAL B 35 LEU B 40 1 1BMD 192 SHEET 3 S1B 6 VAL B 4 THR B 9 1 1BMD 193 SHEET 4 S1B 6 TYR B 82 LEU B 85 1 1BMD 194 SHEET 5 S1B 6 LYS B 124 VAL B 127 1 1BMD 195 SHEET 6 S1B 6 PHE B 151 ALA B 153 1 1BMD 196 SHEET 1 S2B 3 ILE B 177 TRP B 183 0 1BMD 197 SHEET 2 S2B 3 PHE B 191 VAL B 199 -1 1BMD 198 SHEET 3 S2B 3 ARG B 206 PRO B 207 -1 1BMD 199 SHEET 1 S3B 3 VAL B 266 PRO B 271 0 1BMD 200 SHEET 2 S3B 3 VAL B 284 LYS B 292 -1 1BMD 201 SHEET 3 S3B 3 ALA B 295 VAL B 298 -1 1BMD 202 TURN 1 T1 GLY A 10 GLY A 13 1BMD 203 TURN 2 T2 GLY A 30 GLN A 33 1BMD 204 TURN 3 T3 PHE A 61 LEU A 64 1BMD 205 TURN 4 T4 PHE A 77 ALA A 80 1BMD 206 TURN 5 T5 LYS A 92 MET A 95 1BMD 207 TURN 6 T6 LYS A 120 VAL A 123 1BMD 208 TURN 7 T7 ALA A 143 LEU A 146 1BMD 209 TURN 8 T8 ASN A 147 ASN A 150 1BMD 210 TURN 9 T9 PRO A 148 PHE A 151 1BMD 211 TURN 10 T10 GLY A 173 ARG A 176 1BMD 212 TURN 11 T11 VAL A 174 ILE A 177 1BMD 213 TURN 12 T12 SER A 187 MET A 190 1BMD 214 TURN 13 T13 VAL A 199 ARG A 206 1BMD 215 TURN 14 T14 PRO A 261 ASP A 264 1BMD 216 TURN 15 T15 GLY A 274 GLY A 278 1BMD 217 TURN 16 T16 GLU A 275 ILE A 279 1BMD 218 TURN 17 T17 PRO A 280 ILE A 283 1BMD 219 TURN 18 T18 LYS A 292 ALA A 295 1BMD 220 TURN 19 T19 LYS A 327 GLY A 330 1BMD 221 TURN 20 T20 GLY B 10 GLY B 13 1BMD 222 TURN 21 T21 GLY B 30 GLN B 33 1BMD 223 TURN 22 T22 PHE B 61 LEU B 64 1BMD 224 TURN 23 T23 PHE B 77 ALA B 80 1BMD 225 TURN 24 T24 LYS B 92 MET B 95 1BMD 226 TURN 25 T25 LYS B 120 VAL B 123 1BMD 227 TURN 26 T26 ALA B 143 LEU B 146 1BMD 228 TURN 27 T27 ASN B 147 ASN B 150 1BMD 229 TURN 28 T28 PRO B 148 PHE B 151 1BMD 230 TURN 29 T29 GLY B 173 ARG B 176 1BMD 231 TURN 30 T30 VAL B 174 ILE B 177 1BMD 232 TURN 31 T31 SER B 187 MET B 190 1BMD 233 TURN 32 T32 VAL B 199 ARG B 206 1BMD 234 TURN 33 T33 PRO B 261 ASP B 264 1BMD 235 TURN 34 T34 GLY B 274 GLY B 278 1BMD 236 TURN 35 T35 GLU B 275 ILE B 279 1BMD 237 TURN 36 T36 LYS B 292 ALA B 295 1BMD 238 TURN 37 T37 LYS B 327 GLY B 330 1BMD 239 CRYST1 71.510 87.590 118.980 90.00 90.00 90.00 P 21 21 21 8 1BMD 240 ORIGX1 1.000000 0.000000 0.000000 0.00000 1BMD 241 ORIGX2 0.000000 1.000000 0.000000 0.00000 1BMD 242 ORIGX3 0.000000 0.000000 1.000000 0.00000 1BMD 243 SCALE1 0.013984 0.000000 0.000000 0.00000 1BMD 244 SCALE2 0.000000 0.011417 0.000000 0.00000 1BMD 245 SCALE3 0.000000 0.000000 0.008405 0.00000 1BMD 246 MTRIX1 1 -0.606800 0.002100 -0.794800 81.10670 1 1BMD 247 MTRIX2 1 0.003600 -1.000000 -0.005500 50.92750 1 1BMD 248 MTRIX3 1 -0.794800 -0.006200 0.606800 40.36920 1 1BMD 249