HEADER GENE REGULATORY PROTEIN 15-APR-87 3GAP 3GAP 3 COMPND CATABOLITE GENE ACTIVATOR PROTEIN - CYCLIC /AMP$ COMPLEX 3GAP 4 COMPND 2 (/CAP$) 3GAP 5 SOURCE (ESCHERICHIA $COLI) 3GAP 6 AUTHOR I.T.WEBER,T.A.STEITZ 3GAP 7 REVDAT 4 15-JAN-91 3GAPC 3 ATOM 3GAPC 1 REVDAT 3 09-OCT-88 3GAPB 1 FORMUL 3GAPB 1 REVDAT 2 16-JAN-87 3GAPA 1 JRNL 3GAPA 1 REVDAT 1 16-JUL-87 3GAP 0 3GAP 8 SPRSDE 16-JUL-87 3GAP 1GAP 3GAP 9 JRNL AUTH I.T.WEBER,T.A.STEITZ 3GAP 10 JRNL TITL STRUCTURE OF A COMPLEX OF CATABOLITE GENE ACTIVATOR 3GAPA 2 JRNL TITL 2 PROTEIN AND CYCLIC /AMP$ REFINED AT 2.5 ANGSTROMS 3GAPA 3 JRNL TITL 3 RESOLUTION 3GAPA 4 JRNL REF J.MOL.BIOL. V. 198 311 1987 3GAPA 5 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 070 3GAPA 6 REMARK 1 3GAP 16 REMARK 1 REFERENCE 1 3GAP 17 REMARK 1 AUTH I.T.WEBER,G.L.GILLILAND,J.G.HARMAN,A.PETERKOFSKY 3GAP 18 REMARK 1 TITL CRYSTAL STRUCTURE OF A CYCLIC /AMP$-INDEPENDENT 3GAP 19 REMARK 1 TITL 2 MUTANT OF CATABOLITE GENE ACTIVATOR PROTEIN 3GAP 20 REMARK 1 REF J.BIOL.CHEM. V. 262 5630 1987 3GAP 21 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 071 3GAP 22 REMARK 1 REFERENCE 2 3GAP 23 REMARK 1 AUTH I.T.WEBER,T.A.STEITZ 3GAP 24 REMARK 1 TITL A MODEL FOR THE NON-SPECIFIC BINDING OF CATABOLITE 3GAP 25 REMARK 1 TITL 2 GENE ACTIVATOR PROTEIN TO /DNA$ 3GAP 26 REMARK 1 REF NUCLEIC ACIDS RES. V. 12 8475 1984 3GAP 27 REMARK 1 REFN ASTM NARHAD UK ISSN 0305-1048 389 3GAP 28 REMARK 1 REFERENCE 3 3GAP 29 REMARK 1 AUTH I.T.WEBER,T.A.STEITZ 3GAP 30 REMARK 1 TITL MODEL OF SPECIFIC COMPLEX BETWEEN CATABOLITE GENE 3GAP 31 REMARK 1 TITL 2 ACTIVATOR PROTEIN AND B-/DNA$ SUGGESTED BY 3GAP 32 REMARK 1 TITL 3 ELECTROSTATIC COMPLEMENTARITY 3GAP 33 REMARK 1 REF PROC.NAT.ACAD.SCI.USA V. 81 3973 1984 3GAP 34 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 040 3GAP 35 REMARK 1 REFERENCE 4 3GAP 36 REMARK 1 AUTH D.B.MC*KAY,I.T.WEBER,T.A.STEITZ 3GAP 37 REMARK 1 TITL STRUCTURE OF CATABOLITE GENE ACTIVATOR PROTEIN AT 3GAP 38 REMARK 1 TITL 2 2.9-*ANGSTROMS RESOLUTION. INCORPORATION OF AMINO 3GAP 39 REMARK 1 TITL 3 ACID SEQUENCE AND INTERACTIONS WITH CYCLIC /AMP$ 3GAP 40 REMARK 1 REF J.BIOL.CHEM. V. 257 9518 1982 3GAP 41 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 071 3GAP 42 REMARK 1 REFERENCE 5 3GAP 43 REMARK 1 AUTH T.A.STEITZ,D.H.OHLENDORF,D.B.MC*KAY,W.F.ANDERSON, 3GAP 44 REMARK 1 AUTH 2 B.W.MATTHEWS 3GAP 45 REMARK 1 TITL STRUCTURAL SIMILARITY IN THE /DNA$-BINDING DOMAINS 3GAP 46 REMARK 1 TITL 2 OF CATABOLITE GENE ACTIVATOR AND $CRO REPRESSOR 3GAP 47 REMARK 1 TITL 3 PROTEINS 3GAP 48 REMARK 1 REF PROC.NAT.ACAD.SCI.USA V. 79 3097 1982 3GAP 49 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 040 3GAP 50 REMARK 1 REFERENCE 6 3GAP 51 REMARK 1 AUTH D.B.MC*KAY,T.A.STEITZ 3GAP 52 REMARK 1 TITL STRUCTURE OF CATABOLITE GENE ACTIVATOR PROTEIN AT 3GAP 53 REMARK 1 TITL 2 2.9 ANGSTROMS RESOLUTION SUGGESTS BINDING TO 3GAP 54 REMARK 1 TITL 3 LEFT-HANDED B-/DNA$ 3GAP 55 REMARK 1 REF NATURE V. 290 744 1981 3GAP 56 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 006 3GAP 57 REMARK 1 REFERENCE 7 3GAP 58 REMARK 1 AUTH D.B.MC*KAY,M.G.FRIED 3GAP 59 REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION 3GAP 60 REMARK 1 TITL 2 DATA FOR THE CYCLIC /AMP$ RECEPTOR PROTEIN OF 3GAP 61 REMARK 1 TITL 3 ESCHERICHIA $COLI 3GAP 62 REMARK 1 REF J.MOL.BIOL. V. 139 95 1980 3GAP 63 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 070 3GAP 64 REMARK 2 3GAP 65 REMARK 2 RESOLUTION. 2.5 ANGSTROMS. 3GAP 66 REMARK 3 3GAP 67 REMARK 3 REFINEMENT. BY THE USE OF THE RESTRAINED LEAST-SQUARES 3GAP 68 REMARK 3 REFINEMENT PROGRAM *PROLSQ* (J. KONNERT AND 3GAP 69 REMARK 3 W. HENDRICKSON) AND PROGRAM *FREF* (R. W. HARRISON, 1985). 3GAP 70 REMARK 3 THE R-VALUE IS 0.207 FOR REFLECTIONS WITH FOBS .GE. 50 3GAP 71 REMARK 3 IN THE RESOLUTION RANGE 7.0 TO 2.5 ANGSTROMS. THE R VALUE 3GAP 72 REMARK 3 IS 0.256 FOR ALL REFLECTIONS IN THE RANGE 20.0 TO 2.5 3GAP 73 REMARK 3 ANGSTROMS. THE RMS DEVIATION FROM IDEALITY OF THE BOND 3GAP 74 REMARK 3 LENGTHS IS 0.018 ANGSTROMS. THE RMS DEVIATION FROM 3GAP 75 REMARK 3 IDEALITY OF THE BOND ANGLES IS 2.8 DEGREES. ATOMS WITH 3GAP 76 REMARK 3 THERMAL FACTORS WHICH CALCULATE LESS THAN 2.00 ARE 3GAP 77 REMARK 3 ASSIGNED THIS VALUE. THIS IS THE LOWEST VALUE ALLOWED BY 3GAP 78 REMARK 3 THE REFINEMENT PROGRAM. 3GAP 79 REMARK 4 3GAP 80 REMARK 4 THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF A DIMER 3GAP 81 REMARK 4 GIVEN AS CHAINS *A* AND *B* BELOW. EACH MONOMER SUBUNIT 3GAP 82 REMARK 4 CONSISTS OF TWO STRUCTURALLY DISTINCT DOMAINS AND BINDS ONE 3GAP 83 REMARK 4 CAMP. SUBUNIT ONE (CHAIN *A*) IS IN A *CLOSED* 3GAP 84 REMARK 4 CONFORMATION IN WHICH THE N TERMINUS IS CLOSER TO THE C 3GAP 85 REMARK 4 TERMINUS. SUBUNIT TWO (CHAIN *B*) IS IN AN *OPEN* 3GAP 86 REMARK 4 CONFORMATION IN WHICH THE N TERMINUS IS FURTHER FROM THE 3GAP 87 REMARK 4 C TERMINUS. THE LARGER AMINO-TERMINAL DOMAIN IS SEEN TO 3GAP 88 REMARK 4 BIND CYCLIC AMP AND FORMS ALL THE CONTACTS BETWEEN THE 3GAP 89 REMARK 4 SUBUNITS. THE CARBOXY-TERMINAL DOMAIN BINDS TO DNA. IF THE 3GAP 90 REMARK 4 TWO AMINO-TERMINAL DOMAINS ARE SUPERIMPOSED, THE TWO 3GAP 91 REMARK 4 CARBOXY-TERMINAL DOMAINS ARE RELATED BY A ROTATION OF ABOUT 3GAP 92 REMARK 4 30 DEGREES. 3GAP 93 REMARK 5 3GAP 94 REMARK 5 THE SHEET STRUCTURE GIVEN BELOW HAS BEEN DESCRIBED BY THE 3GAP 95 REMARK 5 DEPOSITORS AS A *BETA ROLL*. THE STRANDS HAVE BEEN RENAMED 3GAP 96 REMARK 5 BY THE PROTEIN DATA BANK IN ORDER TO DESCRIBE THE SHEET 3GAP 97 REMARK 5 STRUCTURE CONSISTENT WITH DATA BANK SPECIFICATIONS. 3GAP 98 REMARK 5 THE FOLLOWING TABLE GIVES THE CORRESPONDING STRAND NAMES, 3GAP 99 REMARK 5 3GAP 100 REMARK 5 DEPOSITOR,S ORIGINAL PROTEIN DATA BANK 3GAP 101 REMARK 5 NAME NAME 3GAP 102 REMARK 5 3GAP 103 REMARK 5 1. BETA-1 STRAND 1 AA 3GAP 104 REMARK 5 2. BETA-2 STRAND 1 BA 3GAP 105 REMARK 5 3. BETA-3 STRAND 3 AA 3GAP 106 REMARK 5 4. BETA-4 STRAND 3 BA 3GAP 107 REMARK 5 5. BETA-5 STRAND 4 BA 3GAP 108 REMARK 5 6. BETA-6 STRAND 4 AA 3GAP 109 REMARK 5 7. BETA-7 STRAND 2 BA 3GAP 110 REMARK 5 8. BETA-8 STRAND 2 AA 3GAP 111 REMARK 5 3GAP 112 REMARK 5 THE BETA ROLL CONSISTS OF STRANDS BETA-1, BETA-8, BETA-3 3GAP 113 REMARK 5 AND BETA-6 ON ONE SIDE AND STRANDS BETA-2, BETA-7, BETA-4, 3GAP 114 REMARK 5 AND BETA-5 ON THE OTHER SIDE. 3GAP 115 REMARK 6 3GAP 116 REMARK 6 SITE *S1* CONSTITUTES THE RESIDUES WHICH INTERACT WITH 3GAP 117 REMARK 6 CYCLIC AMP. 3GAP 118 REMARK 7 3GAP 119 REMARK 7 THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW 3GAP 120 REMARK 7 WILL YIELD APPROXIMATE COORDINATES FOR THE AMINO-TERMINAL 3GAP 121 REMARK 7 DOMAIN OF CHAIN *A* WHEN APPLIED TO THE AMINO-TERMINAL 3GAP 122 REMARK 7 DOMAIN OF CHAIN *B*. THE TRANSFORMATION PRESENTED ON 3GAP 123 REMARK 7 *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES 3GAP 124 REMARK 7 FOR THE CARBOXY-TERMINAL DOMAIN OF CHAIN *A* WHEN APPLIED 3GAP 125 REMARK 7 TO THE CARBOXY-TERMINAL DOMAIN OF CHAIN *B*. 3GAP 126 REMARK 8 3GAP 127 REMARK 8 PROTEIN DATA BANK ENTRY 2GAP PRESENTS A COMPLEX BETWEEN 3GAP 128 REMARK 8 THE ACTIVATOR PROTEIN AND A DNA FRAGMENT. 3GAP 129 REMARK 9 3GAPA 7 REMARK 9 CORRECTION. UPDATE JRNL REFERENCE TO REFLECT PUBLICATION. 3GAPA 8 REMARK 9 16-JAN-87. 3GAPA 9 REMARK 10 3GAPB 2 REMARK 10 CORRECTION. FIX FORMAT OF FORMUL RECORD. 09-OCT-88. 3GAPB 3 REMARK 11 3GAPC 2 REMARK 11 CORRECTION. CHANGE ATOM NAMES FROM UNK TO CH2 FOR TRP 3GAPC 3 REMARK 11 RESIDUES. 15-JAN-91. 3GAPC 4 SEQRES 1 A 209 VAL LEU GLY LYS PRO GLN THR ASP PRO THR LEU GLU TRP 3GAP 130 SEQRES 2 A 209 PHE LEU SER HIS CYS HIS ILE HIS LYS TYR PRO SER LYS 3GAP 131 SEQRES 3 A 209 SER THR LEU ILE HIS GLN GLY GLU LYS ALA GLU THR LEU 3GAP 132 SEQRES 4 A 209 TYR TYR ILE VAL LYS GLY SER VAL ALA VAL LEU ILE LYS 3GAP 133 SEQRES 5 A 209 ASP GLU GLU GLY LYS GLU MET ILE LEU SER TYR LEU ASN 3GAP 134 SEQRES 6 A 209 GLN GLY ASP PHE ILE GLY GLU LEU GLY LEU PHE GLU GLU 3GAP 135 SEQRES 7 A 209 GLY GLN GLU ARG SER ALA TRP VAL ARG ALA LYS THR ALA 3GAP 136 SEQRES 8 A 209 CYS GLU VAL ALA GLU ILE SER TYR LYS LYS PHE ARG GLN 3GAP 137 SEQRES 9 A 209 LEU ILE GLN VAL ASN PRO ASP ILE LEU MET ARG LEU SER 3GAP 138 SEQRES 10 A 209 ALA GLN MET ALA ARG ARG LEU GLN VAL THR SER GLU LYS 3GAP 139 SEQRES 11 A 209 VAL GLY ASN LEU ALA PHE LEU ASP VAL THR GLY ARG ILE 3GAP 140 SEQRES 12 A 209 ALA GLN THR LEU LEU ASN LEU ALA LYS GLN PRO ASP ALA 3GAP 141 SEQRES 13 A 209 MET THR HIS PRO ASP GLY MET GLN ILE LYS ILE THR ARG 3GAP 142 SEQRES 14 A 209 GLN GLU ILE GLY GLN ILE VAL GLY CYS SER ARG GLU THR 3GAP 143 SEQRES 15 A 209 VAL GLY ARG ILE LEU LYS MET LEU GLU ASP GLN ASN LEU 3GAP 144 SEQRES 16 A 209 ILE SER ALA HIS GLY LYS THR ILE VAL VAL TYR GLY THR 3GAP 145 SEQRES 17 A 209 ARG 3GAP 146 SEQRES 1 B 209 VAL LEU GLY LYS PRO GLN THR ASP PRO THR LEU GLU TRP 3GAP 147 SEQRES 2 B 209 PHE LEU SER HIS CYS HIS ILE HIS LYS TYR PRO SER LYS 3GAP 148 SEQRES 3 B 209 SER THR LEU ILE HIS GLN GLY GLU LYS ALA GLU THR LEU 3GAP 149 SEQRES 4 B 209 TYR TYR ILE VAL LYS GLY SER VAL ALA VAL LEU ILE LYS 3GAP 150 SEQRES 5 B 209 ASP GLU GLU GLY LYS GLU MET ILE LEU SER TYR LEU ASN 3GAP 151 SEQRES 6 B 209 GLN GLY ASP PHE ILE GLY GLU LEU GLY LEU PHE GLU GLU 3GAP 152 SEQRES 7 B 209 GLY GLN GLU ARG SER ALA TRP VAL ARG ALA LYS THR ALA 3GAP 153 SEQRES 8 B 209 CYS GLU VAL ALA GLU ILE SER TYR LYS LYS PHE ARG GLN 3GAP 154 SEQRES 9 B 209 LEU ILE GLN VAL ASN PRO ASP ILE LEU MET ARG LEU SER 3GAP 155 SEQRES 10 B 209 ALA GLN MET ALA ARG ARG LEU GLN VAL THR SER GLU LYS 3GAP 156 SEQRES 11 B 209 VAL GLY ASN LEU ALA PHE LEU ASP VAL THR GLY ARG ILE 3GAP 157 SEQRES 12 B 209 ALA GLN THR LEU LEU ASN LEU ALA LYS GLN PRO ASP ALA 3GAP 158 SEQRES 13 B 209 MET THR HIS PRO ASP GLY MET GLN ILE LYS ILE THR ARG 3GAP 159 SEQRES 14 B 209 GLN GLU ILE GLY GLN ILE VAL GLY CYS SER ARG GLU THR 3GAP 160 SEQRES 15 B 209 VAL GLY ARG ILE LEU LYS MET LEU GLU ASP GLN ASN LEU 3GAP 161 SEQRES 16 B 209 ILE SER ALA HIS GLY LYS THR ILE VAL VAL TYR GLY THR 3GAP 162 SEQRES 17 B 209 ARG 3GAP 163 HET CMP A 1 21 CYCLIC AMP 3GAP 164 HET CMP B 1 21 CYCLIC AMP 3GAP 165 FORMUL 3 CMP 2(C10 H12 N5 O6 P1) 3GAPB 4 HELIX 1 AA PRO A 9 CYS A 18 1 3GAP 167 HELIX 2 BA TYR A 99 PRO A 110 1 3GAP 168 HELIX 3 CA ILE A 112 GLY A 132 1 3GAP 169 HELIX 4 DA THR A 140 ALA A 151 1 3GAP 170 HELIX 5 EA THR A 168 VAL A 176 1 3GAP 171 HELIX 6 FA ARG A 180 GLU A 191 1 3GAP 172 HELIX 7 AB PRO B 9 CYS B 18 1 3GAP 173 HELIX 8 BB TYR B 99 PRO B 110 1 3GAP 174 HELIX 9 CB ILE B 112 GLU B 129 1 3GAP 175 HELIX 10 DB THR B 140 ALA B 151 1 3GAP 176 HELIX 11 EB THR B 168 VAL B 176 1 3GAP 177 HELIX 12 FB ARG B 180 GLU B 191 1 3GAP 178 SHEET 1 AA 4 HIS A 19 TYR A 23 0 3GAP 179 SHEET 2 AA 4 THR A 90 SER A 98 -1 3GAP 180 SHEET 3 AA 4 GLU A 34 ILE A 42 -1 3GAP 181 SHEET 4 AA 4 ASP A 68 ILE A 70 -1 3GAP 182 SHEET 1 BA 4 SER A 27 GLN A 32 0 3GAP 183 SHEET 2 BA 4 GLU A 77 ALA A 88 -1 3GAP 184 SHEET 3 BA 4 ALA A 48 LYS A 52 -1 3GAP 185 SHEET 4 BA 4 GLU A 58 LEU A 64 -1 3GAP 186 SHEET 1 CA 4 MET A 157 PRO A 160 0 3GAP 187 SHEET 2 CA 4 ASP A 161 ILE A 165 -1 3GAP 188 SHEET 3 CA 4 LYS A 201 VAL A 205 -1 3GAP 189 SHEET 4 CA 4 LEU A 195 HIS A 199 -1 3GAP 190 SHEET 1 AB 4 HIS B 19 TYR B 23 0 3GAP 191 SHEET 2 AB 4 THR B 90 SER B 98 -1 3GAP 192 SHEET 3 AB 4 GLU B 34 ILE B 42 -1 3GAP 193 SHEET 4 AB 4 ASP B 68 ILE B 70 -1 3GAP 194 SHEET 1 BB 4 SER B 27 GLN B 32 0 3GAP 195 SHEET 2 BB 4 GLU B 77 ALA B 88 -1 3GAP 196 SHEET 3 BB 4 ALA B 48 LYS B 52 -1 3GAP 197 SHEET 4 BB 4 GLU B 58 LEU B 64 -1 3GAP 198 SHEET 1 CB 4 MET B 157 PRO B 160 0 3GAP 199 SHEET 2 CB 4 ASP B 161 ILE B 165 -1 3GAP 200 SHEET 3 CB 4 LYS B 201 VAL B 205 -1 3GAP 201 SHEET 4 CB 4 LEU B 195 HIS B 199 -1 3GAP 202 SITE 1 S1A 20 ILE A 30 VAL A 49 LEU A 61 SER A 62 3GAP 203 SITE 2 S1A 20 TYR A 63 LEU A 64 GLY A 71 GLU A 72 3GAP 204 SITE 3 S1A 20 LEU A 73 ARG A 82 SER A 83 ALA A 84 3GAP 205 SITE 4 S1A 20 TRP A 85 VAL A 86 ARG A 123 LEU A 124 3GAP 206 SITE 5 S1A 20 GLN A 125 VAL A 126 THR A 127 SER B 128 3GAP 207 SITE 1 S1B 20 ILE B 30 VAL B 49 LEU B 61 SER B 62 3GAP 208 SITE 2 S1B 20 TYR B 63 LEU B 64 GLY B 71 GLU B 72 3GAP 209 SITE 3 S1B 20 LEU B 73 ARG B 82 SER B 83 ALA B 84 3GAP 210 SITE 4 S1B 20 TRP B 85 VAL B 86 ARG B 123 LEU B 124 3GAP 211 SITE 5 S1B 20 GLN B 125 VAL B 126 THR B 127 SER A 128 3GAP 212 CRYST1 46.500 96.700 105.300 90.00 90.00 90.00 P 21 21 21 8 3GAP 213 ORIGX1 1.000000 0.000000 0.000000 0.00000 3GAP 214 ORIGX2 0.000000 1.000000 0.000000 0.00000 3GAP 215 ORIGX3 0.000000 0.000000 1.000000 0.00000 3GAP 216 SCALE1 .021505 0.000000 0.000000 0.00000 3GAP 217 SCALE2 0.000000 .010341 0.000000 0.00000 3GAP 218 SCALE3 0.000000 0.000000 .009497 0.00000 3GAP 219 MTRIX1 1 -.767190 .004820 -.591410 81.16930 1 3GAP 220 MTRIX2 1 .004690 -1.051440 .051910 86.03960 1 3GAP 221 MTRIX3 1 -.656850 .120330 .741030 26.64350 1 3GAP 222 MTRIX1 2 -.927890 -.030530 -.341610 79.24820 1 3GAP 223 MTRIX2 2 .137650 -.957680 -.313510 90.03610 1 3GAP 224 MTRIX3 2 -.310740 -.328890 .902180 28.15430 1 3GAP 225