HEADER OXIDOREDUCTASE 08-DEC-92 1LGA COMPND LIGNIN PEROXIDASE (LIP) (E.C.1.11.1.-) (FERRIC) SOURCE WHITE ROT BASIDIOMYCETE (PHANEROCHAETE CHRYSOSPORIUM) AUTHOR T.L.POULOS,S.L.EDWARDS,H.WARIISHI,M.H.GOLD REVDAT 1 31-OCT-93 1LGA 0 JRNL AUTH T.L.POULOS,S.L.EDWARDS,H.WARIISHI,M.H.GOLD JRNL TITL CRYSTALLOGRAPHIC REFINEMENT OF LIGNIN PEROXIDASE JRNL TITL 2 AT 2 ANGSTROMS JRNL REF TO BE PUBLISHED JRNL REFN 353 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.L.EDWARDS,R.RAAG,H.WARIISHI,M.H.GOLD,T.L.POULOS REMARK 1 TITL CRYSTAL STRUCTURE OF LIGNIN PEROXIDASE REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN 353 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM X-PLOR REMARK 3 AUTHORS BRUNGER REMARK 3 R VALUE 0.15 REMARK 3 RMSD BOND DISTANCES 0.014 ANGSTROMS REMARK 3 RMSD BOND ANGLES 2.9 DEGREES REMARK 4 REMARK 4 THE MODEL CONSISTS OF A DIMER (I.E. TWO LIP MOLECULES), TWO REMARK 4 CALCIUM IONS PER MONOMER, AND ONE N-ACETYL GLUCOSAMINE REMARK 4 N-LINKED TO ASN 257 PER MONOMER. MOLECULE 1 CONTAINS ALL REMARK 4 343 RESIDUES BUT MOLECULE 2 HAS ONLY RESIDUES 1 - 341. REMARK 4 IN MOLECULE 1 THE SIDE CHAIN OF 342 IS NOT OBSERVED IN THE REMARK 4 MAP AND HAS BEEN EXCLUDED. A LOOP ON THE SURFACE (BOTH REMARK 4 MOLECULES) CENTERED NEAR RESIDUE 60 EXHIBITS VERY HIGH B REMARK 4 FACTORS AND IS POSITIONED DIFFERENTLY IN THE TWO MOLECULES. REMARK 4 THE STRUCTURE OF THIS SURFACE LOOP OUGHT TO BE TAKEN REMARK 4 WITH A LARGE GRAIN OF SALT. REMARK 5 REMARK 5 IN EACH CHAIN GLUCOSAMINE IS LINKED TO ASN 257. REMARK 6 REMARK 6 SER 334 IS LIKELY A SECOND SITE OF GLYCOSYLATION. REMARK 6 ELECTRON DENSITY EXTENDS FROM THIS SIDE CHAIN BUT IS NOT REMARK 6 WELL ENOUGH DEFINED TO FIT CARBOHYDRATE. REMARK 7 REMARK 7 HELIX CONTENT WAS ESTIMATED USING MIKE CARSON'S PROGRAM REMARK 7 RIBBONS. REMARK 8 REMARK 8 THERE ARE FOUR S-S BRIDGES PER MONOMER WITH NO FREE CYS REMARK 8 RESIDUES. REMARK 9 REMARK 9 THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW REMARK 9 WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN REMARK 9 APPLIED TO CHAIN *A*. REMARK 10 REMARK 10 SITES *PHA* AND *PHB*, PRESENTED ON *SITE* RECORDS BELOW, REMARK 10 EACH CONTAIN THE PROXIMAL HEME LIGAND. REMARK 11 REMARK 11 SITES *PBA* AND *PBB*, PRESENTED ON *SITE* RECORDS BELOW, REMARK 11 EACH CONTAIN THE DISTAL RESIDUES FORMING THE PEROXIDE REMARK 11 BINDING POCKET. THIS IS ANALOGOUS TO THE ARG-TRP-HIS FOUND REMARK 11 IN CYTOCHROME C PEROXIDASE. REMARK 12 REMARK 12 SITES *HPA* AND *HPB*, PRESENTED ON *SITE* RECORDS BELOW, REMARK 12 EACH CONTAIN THE RESIDUE THAT H-BONDS WITH PROXIMAL HIS REMARK 12 176. SEQRES 1 A 343 ALA THR CYS ALA ASN GLY LYS THR VAL GLY ASP ALA SER SEQRES 2 A 343 CYS CYS ALA TRP PHE ASP VAL LEU ASP ASP ILE GLN ALA SEQRES 3 A 343 ASN MET PHE HIS GLY GLY GLN CYS GLY ALA GLU ALA HIS SEQRES 4 A 343 GLU SER ILE ARG LEU VAL PHE HIS ASP SER ILE ALA ILE SEQRES 5 A 343 SER PRO ALA MET GLU ALA LYS GLY LYS PHE GLY GLY GLY SEQRES 6 A 343 GLY ALA ASP GLY SER ILE MET ILE PHE ASP THR ILE GLU SEQRES 7 A 343 THR ALA PHE HIS PRO ASN ILE GLY LEU ASP GLU VAL VAL SEQRES 8 A 343 ALA MET GLN LYS PRO PHE VAL GLN LYS HIS GLY VAL THR SEQRES 9 A 343 PRO GLY ASP PHE ILE ALA PHE ALA GLY ALA VAL ALA LEU SEQRES 10 A 343 SER ASN CYS PRO GLY ALA PRO GLN MET ASN PHE PHE THR SEQRES 11 A 343 GLY ARG LYS PRO ALA THR GLN PRO ALA PRO ASP GLY LEU SEQRES 12 A 343 VAL PRO GLU PRO PHE HIS THR VAL ASP GLN ILE ILE ALA SEQRES 13 A 343 ARG VAL ASN ASP ALA GLY GLU PHE ASP GLU LEU GLU LEU SEQRES 14 A 343 VAL TRP MET LEU SER ALA HIS SER VAL ALA ALA VAL ASN SEQRES 15 A 343 ASP VAL ASP PRO THR VAL GLN GLY LEU PRO PHE ASP SER SEQRES 16 A 343 THR PRO GLY ILE PHE ASP SER GLN PHE PHE VAL GLU THR SEQRES 17 A 343 GLN PHE ARG GLY THR LEU PHE PRO GLY SER GLY GLY ASN SEQRES 18 A 343 GLN GLY GLU VAL GLU SER GLY MET ALA GLY GLU ILE ARG SEQRES 19 A 343 ILE GLN THR ASP HIS THR LEU ALA ARG ASP SER ARG THR SEQRES 20 A 343 ALA CYS GLU TRP GLN SER PHE VAL GLY ASN GLN SER LYS SEQRES 21 A 343 LEU VAL ASP ASP PHE GLN PHE ILE PHE LEU ALA LEU THR SEQRES 22 A 343 GLN LEU GLY GLN ASP PRO ASN ALA MET THR ASP CYS SER SEQRES 23 A 343 ASP VAL ILE PRO LEU SER LYS PRO ILE PRO GLY ASN GLY SEQRES 24 A 343 PRO PHE SER PHE PHE PRO PRO GLY LYS SER HIS SER ASP SEQRES 25 A 343 ILE GLU GLN ALA CYS ALA GLU THR PRO PHE PRO SER LEU SEQRES 26 A 343 VAL THR LEU PRO GLY PRO ALA THR SER VAL ALA ARG ILE SEQRES 27 A 343 PRO PRO HIS LYS ALA SEQRES 1 B 343 ALA THR CYS ALA ASN GLY LYS THR VAL GLY ASP ALA SER SEQRES 2 B 343 CYS CYS ALA TRP PHE ASP VAL LEU ASP ASP ILE GLN ALA SEQRES 3 B 343 ASN MET PHE HIS GLY GLY GLN CYS GLY ALA GLU ALA HIS SEQRES 4 B 343 GLU SER ILE ARG LEU VAL PHE HIS ASP SER ILE ALA ILE SEQRES 5 B 343 SER PRO ALA MET GLU ALA LYS GLY LYS PHE GLY GLY GLY SEQRES 6 B 343 GLY ALA ASP GLY SER ILE MET ILE PHE ASP THR ILE GLU SEQRES 7 B 343 THR ALA PHE HIS PRO ASN ILE GLY LEU ASP GLU VAL VAL SEQRES 8 B 343 ALA MET GLN LYS PRO PHE VAL GLN LYS HIS GLY VAL THR SEQRES 9 B 343 PRO GLY ASP PHE ILE ALA PHE ALA GLY ALA VAL ALA LEU SEQRES 10 B 343 SER ASN CYS PRO GLY ALA PRO GLN MET ASN PHE PHE THR SEQRES 11 B 343 GLY ARG LYS PRO ALA THR GLN PRO ALA PRO ASP GLY LEU SEQRES 12 B 343 VAL PRO GLU PRO PHE HIS THR VAL ASP GLN ILE ILE ALA SEQRES 13 B 343 ARG VAL ASN ASP ALA GLY GLU PHE ASP GLU LEU GLU LEU SEQRES 14 B 343 VAL TRP MET LEU SER ALA HIS SER VAL ALA ALA VAL ASN SEQRES 15 B 343 ASP VAL ASP PRO THR VAL GLN GLY LEU PRO PHE ASP SER SEQRES 16 B 343 THR PRO GLY ILE PHE ASP SER GLN PHE PHE VAL GLU THR SEQRES 17 B 343 GLN PHE ARG GLY THR LEU PHE PRO GLY SER GLY GLY ASN SEQRES 18 B 343 GLN GLY GLU VAL GLU SER GLY MET ALA GLY GLU ILE ARG SEQRES 19 B 343 ILE GLN THR ASP HIS THR LEU ALA ARG ASP SER ARG THR SEQRES 20 B 343 ALA CYS GLU TRP GLN SER PHE VAL GLY ASN GLN SER LYS SEQRES 21 B 343 LEU VAL ASP ASP PHE GLN PHE ILE PHE LEU ALA LEU THR SEQRES 22 B 343 GLN LEU GLY GLN ASP PRO ASN ALA MET THR ASP CYS SER SEQRES 23 B 343 ASP VAL ILE PRO LEU SER LYS PRO ILE PRO GLY ASN GLY SEQRES 24 B 343 PRO PHE SER PHE PHE PRO PRO GLY LYS SER HIS SER ASP SEQRES 25 B 343 ILE GLU GLN ALA CYS ALA GLU THR PRO PHE PRO SER LEU SEQRES 26 B 343 VAL THR LEU PRO GLY PRO ALA THR SER VAL ALA ARG ILE SEQRES 27 B 343 PRO PRO HIS LYS ALA HET HEM A 396 43 PROTOPORPHYRIN IX CONTAINS FE(III) HET NAG A 397 14 N-ACETYL-D-GLUCOSAMINE HET CA A 398 1 CALCIUM +2 COUNTER ION HET CA A 399 1 CALCIUM +2 COUNTER ION HET HEM B 396 43 PROTOPORPHYRIN IX CONTAINS FE(III) HET NAG B 397 14 N-ACETYL-D-GLUCOSAMINE HET CA B 398 1 CALCIUM +2 COUNTER ION HET CA B 399 1 CALCIUM +2 COUNTER ION FORMUL 3 HEM 2(C34 H32 N4 O4 FE1 +++) FORMUL 4 NAG 2(C8 H15 N1 O6) FORMUL 5 CA 4(CA1) FORMUL 6 HOH *474(H2 O1) HELIX 1 1A ALA A 16 ASN A 27 1 HELIX 2 2A ALA A 36 SER A 49 1 HELIX 3 3A PRO A 54 GLU A 57 1 HELIX 4 4A SER A 70 GLU A 78 1 HELIX 5 5A LEU A 87 HIS A 101 1 HELIX 6 6A PRO A 105 SER A 118 1 HELIX 7 7A VAL A 151 GLY A 162 1 HELIX 8 8A GLU A 166 MET A 172 1 HELIX 9 9A LEU A 173 SER A 177 5 HELIX 10 10A GLN A 203 GLU A 207 1 HELIX 11 11A GLN A 236 LEU A 241 1 HELIX 12 12A ALA A 248 SER A 253 1 HELIX 13 13A GLN A 258 THR A 273 1 HELIX 14 1B ALA B 16 ASN B 27 1 HELIX 15 2B ALA B 36 SER B 49 1 HELIX 16 3B PRO B 54 GLU B 57 1 HELIX 17 4B SER B 70 GLU B 78 1 HELIX 18 5B LEU B 87 HIS B 101 1 HELIX 19 6B PRO B 105 SER B 118 1 HELIX 20 7B VAL B 151 GLY B 162 1 HELIX 21 8B GLU B 166 MET B 172 1 HELIX 22 9B LEU B 173 SER B 177 5 HELIX 23 10B GLN B 203 GLU B 207 1 HELIX 24 11B GLN B 236 LEU B 241 1 HELIX 25 12B ALA B 248 SER B 253 1 HELIX 26 13B GLN B 258 THR B 273 1 SSBOND 1 CYS A 3 CYS A 15 SSBOND 2 CYS A 14 CYS A 285 SSBOND 3 CYS A 34 CYS A 120 SSBOND 4 CYS A 249 CYS A 317 SSBOND 5 CYS B 3 CYS B 15 SSBOND 6 CYS B 14 CYS B 285 SSBOND 7 CYS B 34 CYS B 120 SSBOND 8 CYS B 249 CYS B 317 SITE 1 PHA 1 HIS A 176 SITE 1 PBA 3 ARG A 43 PHE A 46 HIS A 47 SITE 1 HPA 1 ASP A 238 SITE 1 PHB 1 HIS B 176 SITE 1 PBB 3 ARG B 43 PHE B 46 HIS B 47 SITE 1 HPB 1 ASP B 238 CRYST1 44.700 77.500 100.000 90.00 101.00 90.00 P 21 4 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 0.022371 0.000000 0.004349 0.00000 SCALE2 0.000000 0.012903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010187 0.00000 MTRIX1 1 -0.997900 -0.014110 -0.015300 35.40370 1 MTRIX2 1 0.013920 -0.999800 0.013590 48.66153 1 MTRIX3 1 -0.015510 0.013370 0.999790 49.50549 1