HEADER HYDROLASE 19-FEB-03 1NZT OBSLTE 23-NOV-04 1NZT 1XXE TITLE SOLUTION STRUCTURE OF THE LPXC DEACETYLASE OF LIPID A TITLE 2 BIOSYNTHESIS FROM AQUIFEX AEOLICUS WITH A BOUND SUBSTRATE- TITLE 3 ANALOG INHIBITOR, TU-514 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE COMPND 3 DEACETYLASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: LPXC; UDP-3-0-ACYL N-ACETYLGLCOSAMINE COMPND 6 DEACETYLASE; UDP-3-O-ACYL-GLCNAC DEACETYLASE; COMPND 7 EC: 3.5.1.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 GENE: LPXC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PAALPXC KEYWDS LPXC, TU-514, LIPID A BIOSYNTHESIS, LIPID A, ENDOTOXIN, KEYWDS 2 ENDOTOXIN BIOSYNTHESIS, DEACETYLASE, METALLOAMIDASE, ZINC, KEYWDS 3 UDP-3-O-ACYL-GLCNAC DEACETYLASE, UDP-3-O-(R-3- KEYWDS 4 HYDROXYMYRISTOYL)-N-ACETYLGLUCOSAMINE DEACETYLASE EXPDTA NMR, 15 STRUCTURES AUTHOR B.E.COGGINS,X.LI,A.L.MCCLERREN,O.HINDSGAUL,C.R.H.RAETZ, AUTHOR 2 P.ZHOU REVDAT 3 23-NOV-04 1NZT 1 OBSLTE REVDAT 2 29-JUL-03 1NZT 1 AUTHOR JRNL REMARK REVDAT 1 24-JUN-03 1NZT 0 JRNL AUTH B.E.COGGINS,X.LI,A.L.MCCLERREN,O.HINDSGAUL, JRNL AUTH 2 C.R.H.RAETZ,P.ZHOU JRNL TITL STRUCTURE OF THE LPXC DEACETYLASE WITH A BOUND JRNL TITL 2 SUBSTRATE-ANALOG INHIBITOR JRNL REF NAT.STRUCT.BIOL. V. 10 645 2003 JRNL REFN ASTM NSBIEW US ISSN 1072-8368 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NZT COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PRAGUE ON 18-MAR-2003. REMARK 100 THE RCSB ID CODE IS RCSB018397. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM LPXC/TU-514 U- REMARK 210 15N(LPXC); 25 MM SODIUM PHOSPHATE, PH 6.5; 150 MM POTASSIUM REMARK 210 CHLORIDE; 4 MM DITHIOTHREITOL; 90% H2O, 5% D2O, 5% DMSO; 0.3 REMARK 210 MM LPXC/TU-514 U-13C(LPXC); 25 MM SODIUM PHOSPHATE, PH 6.5; REMARK 210 150 MM POTASSIUM CHLORIDE; 4 MM DITHIOTHREITOL; 95% D2O, 5% REMARK 210 DMSO; 0.3 MM LPXC/TU-514 U-2H/13C/15N(LPXC); 25 MM SODIUM REMARK 210 PHOSPHATE, PH 6.5; 150 MM POTASSIUM CHLORIDE; 4 MM REMARK 210 DITHIOTHREITOL; 90% H2O, 5% D2O, 5% DMSO; 0.3 MM LPXC/TU-514 U REMARK 210 -2H/13C/15N,VIL-METHYL-PROTONATED(LPXC); 25 MM SODIUM REMARK 210 PHOSPHATE, PH 6.5; 150 MM POTASSIUM CHLORIDE; 4 MM REMARK 210 DITHIOTHREITOL; 90% H2O, 5% D2O, 5% DMSO; 0.3 MM LPXC/TU-514 REMARK 210 10%-13C,U-15N(LPXC); 25 MM SODIUM PHOSPHATE, PH 6.5; 150 MM REMARK 210 POTASSIUM CHLORIDE; 4 MM DITHIOTHREITOL; 90% H2O, 5% D2O, 5% REMARK 210 DMSO; 0.3 MM LPXC/TU-514 15N-SELECTIVE LABELING FOR PHE, TYR, REMARK 210 LEU, VAL, ILE OR LYS(LPXC); 25 MM SODIUM PHOSPHATE, PH 6.5; REMARK 210 150 MM POTASSIUM CHLORIDE; 4 MM DITHIOTHREITOL; 90% H2O, 5% REMARK 210 D2O, 5% DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY, METHYL- REMARK 210 METHYL NOESY, F1-13C-FILTERED, REMARK 210 F3-EDITED 3D 13C-NOESY-HSQC, REMARK 210 F1-13C/15N-FILTERED, F3-EDITED REMARK 210 3D 15N-NOESY-HSQC, F1/F2 15N/ REMARK 210 13C-FILTERED 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, XEASY 1.3.3, REMARK 210 TALOS 1999.019.15.47, PACES REMARK 210 1.0, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS/ REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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 2 THR A 85 CB THR A 85 OG1 -0.018 REMARK 500 3 THR A 56 CB THR A 56 OG1 -0.018 REMARK 500 4 LEU A 138 N LEU A 138 CA 0.018 REMARK 500 4 THR A 146 CB THR A 146 OG1 -0.018 REMARK 500 4 THR A 165 CB THR A 165 OG1 -0.018 REMARK 500 5 THR A 85 CB THR A 85 OG1 -0.018 REMARK 500 5 THR A 165 CB THR A 165 OG1 -0.018 REMARK 500 6 THR A 60 CB THR A 60 OG1 -0.018 REMARK 500 6 THR A 71 CB THR A 71 OG1 -0.018 REMARK 500 6 THR A 85 CB THR A 85 OG1 -0.019 REMARK 500 6 LEU A 138 N LEU A 138 CA 0.018 REMARK 500 7 THR A 71 CB THR A 71 OG1 -0.018 REMARK 500 7 THR A 146 CB THR A 146 OG1 -0.019 REMARK 500 8 THR A 71 CB THR A 71 OG1 -0.019 REMARK 500 10 THR A 60 CB THR A 60 OG1 -0.018 REMARK 500 10 THR A 71 CB THR A 71 OG1 -0.018 REMARK 500 10 THR A 179 CB THR A 179 OG1 -0.018 REMARK 500 11 THR A 71 CB THR A 71 OG1 -0.018 REMARK 500 11 THR A 203 CB THR A 203 OG1 -0.017 REMARK 500 12 THR A 150 CB THR A 150 OG1 -0.018 REMARK 500 13 THR A 20 CB THR A 20 OG1 -0.018 REMARK 500 13 THR A 88 CB THR A 88 OG1 -0.018 REMARK 500 14 THR A 179 CB THR A 179 OG1 -0.018 REMARK 500 15 ASN A 94 N ASN A 94 CA 0.019 REMARK 500 15 GLU A 222 C PRO A 223 N 0.020 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 2 VAL A 132 N - CA - C ANGL. DEV. = -3.2 DEGREES REMARK 500 4 VAL A 132 N - CA - C ANGL. DEV. = -4.1 DEGREES REMARK 500 4 GLU A 133 N - CA - C ANGL. DEV. = 4.4 DEGREES REMARK 500 4 ASP A 134 N - CA - C ANGL. DEV. = -3.9 DEGREES REMARK 500 4 GLU A 133 CA - C - N ANGL. DEV. = -3.8 DEGREES REMARK 500 4 ASP A 134 C - N - CA ANGL. DEV. = 3.1 DEGREES REMARK 500 4 LEU A 138 N - CA - C ANGL. DEV. = 3.7 DEGREES REMARK 500 5 THR A 85 CA - CB - CG2 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 VAL A 132 N - CA - C ANGL. DEV. = -3.1 DEGREES REMARK 500 5 GLU A 133 N - CA - C ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ASP A 134 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 5 GLU A 133 CA - C - N ANGL. DEV. = -3.1 DEGREES REMARK 500 6 THR A 85 CA - CB - CG2 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 VAL A 132 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 6 GLU A 133 N - CA - C ANGL. DEV. = 4.3 DEGREES REMARK 500 6 ASP A 134 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 6 GLU A 133 CA - C - N ANGL. DEV. = -3.7 DEGREES REMARK 500 6 ASP A 134 C - N - CA ANGL. DEV. = 3.2 DEGREES REMARK 500 6 LEU A 138 N - CA - C ANGL. DEV. = 3.7 DEGREES REMARK 500 7 THR A 85 CA - CB - CG2 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 THR A 88 CA - CB - CG2 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 THR A 88 CA - CB - CG2 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ASP A 134 N - CA - C ANGL. DEV. = -3.1 DEGREES REMARK 500 10 VAL A 132 N - CA - C ANGL. DEV. = -3.2 DEGREES REMARK 500 10 GLU A 133 N - CA - C ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ASP A 134 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 12 ASP A 134 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 13 ASP A 134 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 15 THR A 85 CA - CB - CG2 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 THR A 88 CA - CB - CG2 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ILE A 92 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 15 THR A 270 CA - CB - CG2 ANGL. DEV. = 3.1 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 1 HIS A 58 -66.26 66.63 REMARK 500 2 HIS A 58 -67.58 63.89 REMARK 500 3 HIS A 58 -66.84 66.79 REMARK 500 4 HIS A 58 -61.12 69.49 REMARK 500 5 HIS A 58 -65.85 67.45 REMARK 500 6 HIS A 58 -69.76 62.98 REMARK 500 7 HIS A 58 -67.38 65.32 REMARK 500 8 HIS A 58 -66.31 66.10 REMARK 500 9 HIS A 58 -68.17 65.20 REMARK 500 10 HIS A 58 -62.41 68.85 REMARK 500 11 HIS A 58 -65.36 67.61 REMARK 500 12 HIS A 58 -67.35 65.37 REMARK 500 13 HIS A 58 -65.75 67.51 REMARK 500 14 HIS A 58 -67.22 64.81 REMARK 500 15 HIS A 58 -62.83 68.93 DBREF 1NZT A 1 282 UNP O67648 LPXC_AQUAE 1 282 SEQRES 1 A 282 MET GLY LEU GLU LYS THR VAL LYS GLU LYS LEU SER PHE SEQRES 2 A 282 GLU GLY VAL GLY ILE HIS THR GLY GLU TYR SER LYS LEU SEQRES 3 A 282 ILE ILE HIS PRO GLU LYS GLU GLY THR GLY ILE ARG PHE SEQRES 4 A 282 PHE LYS ASN GLY VAL TYR ILE PRO ALA ARG HIS GLU PHE SEQRES 5 A 282 VAL VAL HIS THR ASN HIS SER THR ASP LEU GLY PHE LYS SEQRES 6 A 282 GLY GLN ARG ILE LYS THR VAL GLU HIS ILE LEU SER VAL SEQRES 7 A 282 LEU HIS LEU LEU GLU ILE THR ASN VAL THR ILE GLU VAL SEQRES 8 A 282 ILE GLY ASN GLU ILE PRO ILE LEU ASP GLY SER GLY TRP SEQRES 9 A 282 GLU PHE TYR GLU ALA ILE ARG LYS ASN ILE LEU ASN GLN SEQRES 10 A 282 ASN ARG GLU ILE ASP TYR PHE VAL VAL GLU GLU PRO ILE SEQRES 11 A 282 ILE VAL GLU ASP GLU GLY ARG LEU ILE LYS ALA GLU PRO SEQRES 12 A 282 SER ASP THR LEU GLU VAL THR TYR GLU GLY GLU PHE LYS SEQRES 13 A 282 ASN PHE LEU GLY ARG GLN LYS PHE THR PHE VAL GLU GLY SEQRES 14 A 282 ASN GLU GLU GLU ILE VAL LEU ALA ARG THR PHE CYS PHE SEQRES 15 A 282 ASP TRP GLU ILE GLU HIS ILE LYS LYS VAL GLY LEU GLY SEQRES 16 A 282 LYS GLY GLY SER LEU LYS ASN THR LEU VAL LEU GLY LYS SEQRES 17 A 282 ASP LYS VAL TYR ASN PRO GLU GLY LEU ARG TYR GLU ASN SEQRES 18 A 282 GLU PRO VAL ARG HIS LYS VAL PHE ASP LEU ILE GLY ASP SEQRES 19 A 282 LEU TYR LEU LEU GLY SER PRO VAL LYS GLY LYS PHE TYR SEQRES 20 A 282 SER PHE ARG GLY GLY HIS SER LEU ASN VAL LYS LEU VAL SEQRES 21 A 282 LYS GLU LEU ALA LYS LYS GLN LYS LEU THR ARG ASP LEU SEQRES 22 A 282 PRO HIS LEU PRO SER VAL GLN ALA LEU HET ZN 336 1 HET TUX 320 71 HETNAM ZN ZINC ION HETNAM TUX 1,5-ANHYDRO-2-C-(CARBOXYMETHYL-N-HYDROXYAMIDE)-2- HETNAM 2 TUX DEOXY-3-O-MYRISTOYL-D-GLUCITOL HETSYN TUX TU-514 FORMUL 2 ZN ZN 2+ FORMUL 3 TUX C22 H41 N O7 HELIX 1 1 GLU A 73 LEU A 82 1 10 HELIX 2 2 TRP A 104 ASN A 113 1 10 HELIX 3 3 GLU A 172 LEU A 176 5 5 HELIX 4 4 ASP A 183 LYS A 190 1 8 HELIX 5 5 GLY A 195 GLY A 198 5 4 HELIX 6 6 ASN A 213 GLY A 216 5 4 HELIX 7 7 GLU A 222 LEU A 237 1 16 HELIX 8 8 HIS A 253 LYS A 268 1 16 SHEET 1 A 2 GLU A 4 VAL A 7 0 SHEET 2 A 2 ILE A 114 GLN A 117 -1 O LEU A 115 N THR A 6 SHEET 1 B 5 LEU A 11 VAL A 16 0 SHEET 2 B 5 TYR A 23 HIS A 29 -1 O ILE A 28 N LEU A 11 SHEET 3 B 5 VAL A 87 ILE A 92 -1 O THR A 88 N HIS A 29 SHEET 4 B 5 ILE A 37 LYS A 41 1 N ARG A 38 O VAL A 87 SHEET 5 B 5 VAL A 44 ALA A 48 -1 O VAL A 44 N LYS A 41 SHEET 1 C 3 HIS A 55 THR A 56 0 SHEET 2 C 3 THR A 60 PHE A 64 -1 N ASP A 61 O HIS A 55 SHEET 3 C 3 GLN A 67 ILE A 69 -1 N ILE A 69 O LEU A 62 SHEET 1 D 2 PHE A 124 VAL A 125 0 SHEET 2 D 2 VAL A 242 LYS A 243 1 N LYS A 243 O PHE A 124 SHEET 1 E 5 ILE A 130 ASP A 134 0 SHEET 2 E 5 ARG A 137 PRO A 143 -1 O ALA A 141 N ILE A 130 SHEET 3 E 5 LYS A 245 PHE A 249 -1 O LYS A 245 N GLU A 142 SHEET 4 E 5 GLU A 148 GLY A 153 1 O GLU A 148 N PHE A 246 SHEET 5 E 5 GLN A 162 PHE A 166 -1 O PHE A 164 N TYR A 151 SHEET 1 F 2 THR A 179 PHE A 182 0 SHEET 2 F 2 THR A 203 LEU A 206 1 O LEU A 204 N CYS A 181 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