PDB:1BQW HEADER POLYVALENT PEROXIDASE 19-AUG-98 1BQW TITLE MOLECULAR MODEL OF A POLYVALENT PEROXIDASE ISOLATED FROM TITLE 2 PARTIALLY-DELIGNIFIED LIGNOCELLULOSE WHICH INCLUDES BOTH TITLE 3 MNP AND LIP-TYPE BINDING SITES, THEORETICAL MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIDASE; COMPND 3 CHAIN: NULL; COMPND 4 EC: 1.11.1.13, 1.11.1.7, 1.11.1.14 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS ERYNGII; SOURCE 3 ORGANISM_COMMON: THISTLE MUSHROOM; SOURCE 4 STRAIN: IJFM A169; SOURCE 5 COLLECTION: ATCC 90787, CBS 613.91; SOURCE 6 ORGAN: HETEROKARYOTIC MYCELIUM; SOURCE 7 GENE: PS1 KEYWDS POLYVALENT PEROXIDASE, MANGANESE PEROXIDASE (MNP), KEYWDS 2 LIGNIN PEROXIDASE (LIP), LIGNIN DEGRADATION, OXIDATION, KEYWDS 3 SUBSTRATE BINDING SITES, CLASS II (FUNGAL) PEROXIDASES EXPDTA THEORETICAL MODEL AUTHOR A.T.MARTINEZ,S.SARKAR,F.J.RUIZ-DUENAS,S.CAMARERO, AUTHOR 2 M.J.MARTINEZ REVDAT 1 18-MAY-99 1BQW 0 JRNL AUTH S.CAMARERO,S.SARKAR,F.J.RUIZ-DUENAS,M.J.MARTINEZ, JRNL AUTH 2 A.T.MARTINEZ JRNL TITL DESCRIPTION OF A VERSATILE PEROXIDASE INVOLVED IN JRNL TITL 2 THE NATURAL DEGRADATION OF LIGNIN THAT HAS BOTH JRNL TITL 3 MANGANESE PEROXIDASE AND LIGNIN PEROXIDASE JRNL TITL 4 SUBSTRATE INTERACTION SITES JRNL REF J.BIOL.CHEM. V. 274 10324 1999 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 0071 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM REMARK 3 AUTHORS : BROOKS ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BQW COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: REMARK 220 MODELLING PROGRAM: PROMOD REMARK 220 PROGRAM AUTHORS: M.C.PEITSCH REMARK 220 MODELLING EXPERIMENT: - THIS MODEL IS BASED UPON THE REMARK 220 COORDINATES OF 1QPA (X-RAY DIFFRACTION), 1ARP REMARK 220 (X-RAY DIFFRACTION), 1LGA (X-RAY DIFFRACTION), 1MNP REMARK 220 (X-RAY DIFFRACTION (FOLLOWED BY CHARMM REFINING) - PROMOD 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 400 REMARK 400 COMPOUND REMARK 400 THIS POLYVALENT PEROXIDASE CAN OXIDIZE MN(II) REMARK 400 (EC 1.11.1.13, MNP), HYDROQUINONES AND SUBSTITUTED PHENOLS REMARK 400 (EC 1.11.1.7, PEROXIDASE), AND VERATRYL ALCOHOL AND REMARK 400 1,4-DIMETHOXYBENZENE (EC 1.11.1.14, LIP), AND IS PRODUCED REMARK 400 ONLY DURING FUNGAL DELIGNIFICATION OF A NATURAL REMARK 400 LIGNOCELLULOSIC SUBSTRATE UNDER SOLID-STATE FERMENTATION REMARK 400 CONDITIONS. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL 287 O REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: VBS REMARK 800 SITE_DESCRIPTION: RESIDUES AT HEME CHANNEL EDGE REMARK 800 INCLUDING VERATRYL ALCOHOL BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: HPR REMARK 800 SITE_DESCRIPTION: HEME POCKET CHARACTERISTIC RESIDUES REMARK 800 REMARK 800 SITE_IDENTIFIER: MBS REMARK 800 SITE_DESCRIPTION: MN(II) BINDING SITE DBREF 1BQW 1 287 PDB 1BQW 1BQW 1 287 SEQRES 1 287 VAL THR CYS ALA THR GLY GLN THR THR ALA ASN GLU ALA SEQRES 2 287 CYS CYS ALA LEU PHE PRO ILE LEU ASP ASP ILE GLN THR SEQRES 3 287 ASN PHE PHE ASP GLY ALA GLN CYS GLY GLU GLU VAL HIS SEQRES 4 287 GLU SER LEU ARG LEU THR PHE HIS ASP ALA ILE ALA PHE SEQRES 5 287 SER PRO ALA LEU THR ASN ALA GLY GLN PHE GLY GLY GLY SEQRES 6 287 GLY ALA ASP GLY SER MET ILE ILE PHE SER ASP THR GLU SEQRES 7 287 PRO ASN PHE HIS ALA ASN LEU GLY ILE ASP GLU ILE VAL SEQRES 8 287 GLU ALA GLN LYS PRO PHE ILE ALA ARG HIS ASN ILE SER SEQRES 9 287 ALA ALA ASP LEU ILE GLN PHE ALA GLY ALA ILE GLY VAL SEQRES 10 287 SER ASN CYS ALA GLY ALA PRO ARG LEU ASN PHE PHE LEU SEQRES 11 287 GLY ARG PRO ASP ALA THR GLN ILE PRO PRO ASP GLY LEU SEQRES 12 287 VAL PRO GLU PRO PHE ASP ASP VAL THR LYS ILE LEU SER SEQRES 13 287 ARG MET GLY ASP ALA GLY PHE SER THR VAL GLU VAL VAL SEQRES 14 287 TRP LEU LEU ALA SER HIS THR ILE ALA ALA ALA ASP HIS SEQRES 15 287 VAL ASP PRO SER ILE PRO GLY THR PRO PHE ASP SER THR SEQRES 16 287 PRO SER THR PHE ASP SER GLN PHE PHE LEU GLU THR MET SEQRES 17 287 LEU GLN GLY THR ALA PHE PRO GLY THR PRO GLY ASN GLN SEQRES 18 287 GLY GLU VAL GLU SER PRO LEU ALA GLY GLU MET ARG LEU SEQRES 19 287 GLN SER ASP PHE LEU LEU ALA ARG ASP SER ARG SER ALA SEQRES 20 287 CYS GLU TRP GLN SER MET VAL ASN ASN MET PRO LYS ILE SEQRES 21 287 GLN ASN ARG PHE THR GLN VAL MET LYS LYS LEU SER ILE SEQRES 22 287 LEU GLY HIS ASN GLN ALA ASP LEU ILE ASP CYS SER ASP SEQRES 23 287 VAL HELIX 1 1 GLU 12 ASN 27 5 16 HELIX 2 2 GLU 36 ALA 49 1 14 HELIX 3 3 PRO 54 ALA 59 1 6 HELIX 4 4 SER 70 ILE 73 1 4 HELIX 5 5 SER 75 ASN 80 1 6 HELIX 6 6 HIS 82 ASN 84 5 3 HELIX 7 7 ASP 88 HIS 101 1 14 HELIX 8 8 ALA 105 ASN 119 1 15 HELIX 9 9 VAL 151 ALA 161 1 11 HELIX 10 10 THR 165 ILE 177 1 13 HELIX 11 11 GLN 202 MET 208 1 7 HELIX 12 12 GLN 235 LEU 240 1 6 HELIX 13 13 ALA 247 MET 253 1 7 HELIX 14 14 MET 257 ILE 273 1 17 HELIX 15 15 GLN 278 ASP 280 5 3 SSBOND 1 CYS 3 CYS 15 SSBOND 2 CYS 14 CYS 284 SSBOND 3 CYS 34 CYS 120 SITE 1 VBS 8 HIS 82 GLU 146 PHE 148 GLN 221 SITE 2 VBS 8 ASN 220 VAL 183 HIS 182 LEU 85 SITE 1 HPR 8 ARG 43 PHE 46 HIS 47 GLU 78 SITE 2 HPR 8 ASN 84 HIS 175 PHE 192 ASP 237 SITE 1 MBS 3 GLU 36 GLU 40 ASP 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 ATOM 1 N VAL 1 21.657 3.838 22.961 1.00 28.33 N 199808191MJRNL AUTH S.CAMARERO,S.SARKAR,F.J.RUIZ-DUENAS,M.J.MARTINEZ, JRNL AUTH 2 A.T.MARTINEZ JRNL TITL DESCRIPTION OF A VERSATILE PEROXIDASE INVOLVED IN JRNL TITL 2 THE NATURAL DEGRADATION OF LIGNIN THAT HAS BOTH JRNL TITL 3 MANGANESE PEROXIDASE AND LIGNIN PEROXIDASE JRNL TITL 4 SUBSTRATE INTERACTION SITES JRNL REF J.BIOL.CHEM. V. 274 10324 1999 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 0071 999.0000001.0001.0001.00090.0090.0090.00P 1HELIX 1 1 GLU 12 ASN 27 5 16 HELIX 2 2 GLU 36 ALA 49 1 14 HELIX 3 3 PRO 54 ALA 59 1 6 HELIX 4 4 SER 70 ILE 73 1 4 HELIX 5 5 SER 75 ASN 80 1 6 HELIX 6 6 HIS 82 ASN 84 5 3 HELIX 7 7 ASP 88 HIS 101 1 14 HELIX 8 8 ALA 105 ASN 119 1 15 HELIX 9 9 VAL 151 ALA 161 1 11 HELIX 10 10 THR 165 ILE 177 1 13 HELIX 11 11 GLN 202 MET 208 1 7 HELIX 12 12 GLN 235 LEU 240 1 6 HELIX 13 13 ALA 247 MET 253 1 7 HELIX 14 14 MET 257 ILE 273 1 17 HELIX 15 15 GLN 278 ASP 280 5 3 ID VBS DESCR RESID HIS 82 RESID GLU 146 RESID PHE 148 RESID GLN 221 RESID ASN 220 RESID VAL 183 RESID HIS 182 RESID LEU 85 ID HPR DESCR RESID ARG 43 RESID PHE 46 RESID HIS 47 RESID GLU 78 RESID ASN 84 RESID HIS 175 RESID PHE 192 RESID ASP 237 ID MBS DESCR RESID GLU 36 RESID GLU 40 RESID ASP 181 HEADER POLYVALENT PEROXIDASE 19-AUG-98 1BQW TITLE MOLECULAR MODEL OF A POLYVALENT PEROXIDASE ISOLATED FROM TITLE 2 PARTIALLY-DELIGNIFIED LIGNOCELLULOSE WHICH INCLUDES BOTH TITLE 3 MNP AND LIP-TYPE BINDING SITES, THEORETICAL MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIDASE; COMPND 3 CHAIN: NULL; COMPND 4 EC: 1.11.1.13, 1.11.1.7, 1.11.1.14 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLEUROTUS ERYNGII; SOURCE 3 ORGANISM_COMMON: THISTLE MUSHROOM; SOURCE 4 STRAIN: IJFM A169; SOURCE 5 COLLECTION: ATCC 90787, CBS 613.91; SOURCE 6 ORGAN: HETEROKARYOTIC MYCELIUM; SOURCE 7 GENE: PS1 KEYWDS POLYVALENT PEROXIDASE, MANGANESE PEROXIDASE (MNP), KEYWDS 2 LIGNIN PEROXIDASE (LIP), LIGNIN DEGRADATION, OXIDATION, KEYWDS 3 SUBSTRATE BINDING SITES, CLASS II (FUNGAL) PEROXIDASES EXPDTA THEORETICAL MODEL AUTHOR A.T.MARTINEZ,S.SARKAR,F.J.RUIZ-DUENAS,S.CAMARERO, AUTHOR 2 M.J.MARTINEZ REVDAT 1 18-MAY-99 1BQW 0 JRNL AUTH S.CAMARERO,S.SARKAR,F.J.RUIZ-DUENAS,M.J.MARTINEZ, JRNL AUTH 2 A.T.MARTINEZ JRNL TITL DESCRIPTION OF A VERSATILE PEROXIDASE INVOLVED IN JRNL TITL 2 THE NATURAL DEGRADATION OF LIGNIN THAT HAS BOTH JRNL TITL 3 MANGANESE PEROXIDASE AND LIGNIN PEROXIDASE JRNL TITL 4 SUBSTRATE INTERACTION SITES JRNL REF J.BIOL.CHEM. V. 274 10324 1999 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 0071 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM REMARK 3 AUTHORS : BROOKS ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BQW COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: REMARK 220 MODELLING PROGRAM: PROMOD REMARK 220 PROGRAM AUTHORS: M.C.PEITSCH REMARK 220 MODELLING EXPERIMENT: - THIS MODEL IS BASED UPON THE REMARK 220 COORDINATES OF 1QPA (X-RAY DIFFRACTION), 1ARP REMARK 220 (X-RAY DIFFRACTION), 1LGA (X-RAY DIFFRACTION), 1MNP REMARK 220 (X-RAY DIFFRACTION (FOLLOWED BY CHARMM REFINING) - PROMOD 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 400 REMARK 400 COMPOUND REMARK 400 THIS POLYVALENT PEROXIDASE CAN OXIDIZE MN(II) REMARK 400 (EC 1.11.1.13, MNP), HYDROQUINONES AND SUBSTITUTED PHENOLS REMARK 400 (EC 1.11.1.7, PEROXIDASE), AND VERATRYL ALCOHOL AND REMARK 400 1,4-DIMETHOXYBENZENE (EC 1.11.1.14, LIP), AND IS PRODUCED REMARK 400 ONLY DURING FUNGAL DELIGNIFICATION OF A NATURAL REMARK 400 LIGNOCELLULOSIC SUBSTRATE UNDER SOLID-STATE FERMENTATION REMARK 400 CONDITIONS. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL 287 O REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: VBS REMARK 800 SITE_DESCRIPTION: RESIDUES AT HEME CHANNEL EDGE REMARK 800 INCLUDING VERATRYL ALCOHOL BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: HPR REMARK 800 SITE_DESCRIPTION: HEME POCKET CHARACTERISTIC RESIDUES REMARK 800 REMARK 800 SITE_IDENTIFIER: MBS REMARK 800 SITE_DESCRIPTION: MN(II) BINDING SITE DBREF 1BQW 1 287 PDB 1BQW 1BQW 1 287 SEQRES 1 287 VAL THR CYS ALA THR GLY GLN THR THR ALA ASN GLU ALA SEQRES 2 287 CYS CYS ALA LEU PHE PRO ILE LEU ASP ASP ILE GLN THR SEQRES 3 287 ASN PHE PHE ASP GLY ALA GLN CYS GLY GLU GLU VAL HIS SEQRES 4 287 GLU SER LEU ARG LEU THR PHE HIS ASP ALA ILE ALA PHE SEQRES 5 287 SER PRO ALA LEU THR ASN ALA GLY GLN PHE GLY GLY GLY SEQRES 6 287 GLY ALA ASP GLY SER MET ILE ILE PHE SER ASP THR GLU SEQRES 7 287 PRO ASN PHE HIS ALA ASN LEU GLY ILE ASP GLU ILE VAL SEQRES 8 287 GLU ALA GLN LYS PRO PHE ILE ALA ARG HIS ASN ILE SER SEQRES 9 287 ALA ALA ASP LEU ILE GLN PHE ALA GLY ALA ILE GLY VAL SEQRES 10 287 SER ASN CYS ALA GLY ALA PRO ARG LEU ASN PHE PHE LEU SEQRES 11 287 GLY ARG PRO ASP ALA THR GLN ILE PRO PRO ASP GLY LEU SEQRES 12 287 VAL PRO GLU PRO PHE ASP ASP VAL THR LYS ILE LEU SER SEQRES 13 287 ARG MET GLY ASP ALA GLY PHE SER THR VAL GLU VAL VAL SEQRES 14 287 TRP LEU LEU ALA SER HIS THR ILE ALA ALA ALA ASP HIS SEQRES 15 287 VAL ASP PRO SER ILE PRO GLY THR PRO PHE ASP SER THR SEQRES 16 287 PRO SER THR PHE ASP SER GLN PHE PHE LEU GLU THR MET SEQRES 17 287 LEU GLN GLY THR ALA PHE PRO GLY THR PRO GLY ASN GLN SEQRES 18 287 GLY GLU VAL GLU SER PRO LEU ALA GLY GLU MET ARG LEU SEQRES 19 287 GLN SER ASP PHE LEU LEU ALA ARG ASP SER ARG SER ALA SEQRES 20 287 CYS GLU TRP GLN SER MET VAL ASN ASN MET PRO LYS ILE SEQRES 21 287 GLN ASN ARG PHE THR GLN VAL MET LYS LYS LEU SER ILE SEQRES 22 287 LEU GLY HIS ASN GLN ALA ASP LEU ILE ASP CYS SER ASP SEQRES 23 287 VAL HELIX 1 1 GLU 12 ASN 27 5 16 HELIX 2 2 GLU 36 ALA 49 1 14 HELIX 3 3 PRO 54 ALA 59 1 6 HELIX 4 4 SER 70 ILE 73 1 4 HELIX 5 5 SER 75 ASN 80 1 6 HELIX 6 6 HIS 82 ASN 84 5 3 HELIX 7 7 ASP 88 HIS 101 1 14 HELIX 8 8 ALA 105 ASN 119 1 15 HELIX 9 9 VAL 151 ALA 161 1 11 HELIX 10 10 THR 165 ILE 177 1 13 HELIX 11 11 GLN 202 MET 208 1 7 HELIX 12 12 GLN 235 LEU 240 1 6 HELIX 13 13 ALA 247 MET 253 1 7 HELIX 14 14 MET 257 ILE 273 1 17 HELIX 15 15 GLN 278 ASP 280 5 3 SSBOND 1 CYS 3 CYS 15 SSBOND 2 CYS 14 CYS 284 SSBOND 3 CYS 34 CYS 120 SITE 1 VBS 8 HIS 82 GLU 146 PHE 148 GLN 221 SITE 2 VBS 8 ASN 220 VAL 183 HIS 182 LEU 85 SITE 1 HPR 8 ARG 43 PHE 46 HIS 47 GLU 78 SITE 2 HPR 8 ASN 84 HIS 175 PHE 192 ASP 237 SITE 1 MBS 3 GLU 36 GLU 40 ASP 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 ATOM 1 N VAL 1 21.657 3.838 22.961 1.00 28.33 N