HEADER TRANSCRIPTION/DNA 02-FEB-99 1QAA TITLE KNOWLEDGE BASED MODEL OF A LEXA REPRESSOR DIMER TITLE 2 (THEORETICAL MODEL) BOUND TO RECA OPERATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 D(P*TP*AP*CP*TP*GP*TP*AP*TP*GP*AP*GP*CP*AP*TP*AP*CP*AP*GP*T COMPND 4 P*A)-3'; COMPND 5 CHAIN: C; COMPND 6 SYNONYM: RECA OPERATOR; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'- COMPND 10 D(P*TP*AP*CP*TP*GP*TP*AP*TP*GP*CP*TP*CP*AP*TP*AP*CP*AP*GP*T COMPND 11 P*A)-3'; COMPND 12 CHAIN: D; COMPND 13 SYNONYM: RECA OPERATOR; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: LEXA REPRESSOR; COMPND 17 CHAIN: A, B; COMPND 18 FRAGMENT: RESIDUES 1-202 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_COMMON: BACTERIA; SOURCE 8 OTHER_DETAILS: THEORETICAL MODEL KEYWDS LEXA REPRESSOR DIMER RECA OPERATOR COMPLEX, SOS RESPONSE, KEYWDS 2 TRANSCRIPTION REGULATION EXPDTA THEORETICAL MODEL AUTHOR R.CHATTOPADHYAYA,K.GHOSH REVDAT 4 14-SEP-04 1QAA 1 REMARK REVDAT 3 01-APR-03 1QAA 1 JRNL REVDAT 2 27-APR-01 1QAA 1 JRNL HEADER REMARK REVDAT 1 02-FEB-99 1QAA 0 JRNL AUTH R.CHATTOPADHYAYA,K.GHOSH,V.M.NAMBOODIRI JRNL TITL MODEL OF A LEXA REPRESSOR DIMER BOUND TO RECA JRNL TITL 2 OPERATOR JRNL REF J.BIOMOL.STRUCT.DYN. V. 18 181 2000 JRNL REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.FOGH,G.OTTLEBEN,H.RUTERJANS,M.SCHNARR,R.BOELENS, REMARK 1 AUTH 2 R.KAPTEIN REMARK 1 TITL SOLUTION STRUCTURE OF THE LEXA REPRESSOR DNA REMARK 1 TITL 2 BINDIN DOMAIN DETERMINED BY 1H NMR SPECTROSCOPY REMARK 1 REF EMBO J. V. 13 3936 1994 REMARK 1 REFN ASTM EMJODG UK ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.M.A.KNEGTEL,R.H.FOGH,G.OTTLEBEN,H.RUTERJANS, REMARK 1 AUTH 2 P.DUMUOLIN,M.SCHNARR,R.BOELENS,R.KAPTEIN REMARK 1 TITL A MODEL FOR THE LEXA REPRESSOR DNA COMPLEX REMARK 1 REF PROTEINS: STRUCT., FUNCT., V. 21 226 1995 REMARK 1 REF 2 GENET. REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.S.PEAT,E.G.FRANK,J.P.MCDONALD,A.S.LEVINE, REMARK 1 AUTH 2 R.WOODGATE,W.A.HENDRICKSON REMARK 1 TITL STRUCTURE OF THE UMUD' PROTEIN AND ITS REGULATION REMARK 1 TITL 2 IN RESPONSE TO DNA DAMAGE REMARK 1 REF NATURE V. 380 727 1996 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH J.W.LITTLE REMARK 1 TITL AUTODIGESTION OF LEXA AND PHAGE LAMBDA REPRESSORS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 81 1375 1984 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 5 REMARK 1 AUTH J.W.LITTLE,S.A.HILL REMARK 1 TITL DELETIONS WITHIN A HINGE REGION OF A SPECIFIC DNA REMARK 1 TITL 2 BINDING PROTEIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 82 2301 1985 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 6 REMARK 1 AUTH S.N.SLILATY,J.A.RUPLEY,J.W.LITTLE REMARK 1 TITL INTRAMOLECULAR CLEAVAGE OF LEXA AND PHAGE LAMBDA REMARK 1 TITL 2 REPRESSORS : DEPENDENCE OF KINETICS ON REPRESSOR REMARK 1 TITL 3 CONCENTRATION, PH, TEMPERATURE AND SOLVENT REMARK 1 REF BIOCHEMISTRY V. 25 6866 1986 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 7 REMARK 1 AUTH S.N.SLILATY,J.W.LITTLE REMARK 1 TITL LYSINE-156 AND SERINE-119 ARE REQUIRED FOR LEXA REMARK 1 TITL 2 REPRESSOR CLEAVAGE : A POSSIBLE MECHANISM REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 84 3987 1987 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 8 REMARK 1 AUTH K.L.ROLAND,M.H.SMITH,J.A.RUPLEY,J.W.LITTLE REMARK 1 TITL IN VITRO ANALYSIS OF MUTANT LEXA PROTEINS WITH AN REMARK 1 TITL 2 INCREASED RATE OF SPECIFIC CLEAVAGE REMARK 1 REF J.MOL.BIOL. V. 228 395 1992 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 9 REMARK 1 AUTH M.H.SMITH,M.M.CAVENAGH,J.W.LITTLE REMARK 1 TITL MUTANT LEXA PROTEINS WITH AN INCREASED RATE OF IN REMARK 1 TITL 2 VIVO CLEAVAGE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 88 7356 1991 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 10 REMARK 1 AUTH K.L.ROLAND,J.W.LITTLE REMARK 1 TITL REACTION OF LEXA REPRESSOR WITH DIISOPROPYL REMARK 1 TITL 2 FLUOROPHOSPHATE : A TEST OF THE SERINE PROTEASE REMARK 1 TITL 3 MODEL REMARK 1 REF J.BIOL.CHEM. V. 265 12828 1990 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 11 REMARK 1 AUTH D.P.SHEPLEY,J.W.LITTLE REMARK 1 TITL MUTANT LEXA PROTEINS WITH SPECIFIC DEFECTS IN REMARK 1 TITL 2 AUTODIGESTION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 93 11528 1996 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REFERENCE 12 REMARK 1 AUTH R.CHATTOPADHYAYA,A.PAL REMARK 1 TITL IMPROVED MODEL OF A LEXA REPRESSOR DIMER BOUND TO REMARK 1 TITL 2 RECA OPERATOR REMARK 1 REF J.BIOMOL.STRUCT.DYN. V. 21 681 2004 REMARK 1 REFN ASTM JBSDD6 US ISSN 0739-1102 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QAA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 THE E.COLI LEXA REPRESSOR IS A TWO DOMAIN, 202 AMINO ACID REMARK 6 PROTEIN CONTROLLING ABOUT 20 UNLINKED GENES COMPRISING REMARK 6 THE BACTERIAL SOS RESPONSE. AN NMR STRUCTURE FOR REMARK 6 RESIDUES 1-72 IS AVAILABLE (PDB CODE 1LEA; ALSO REF. 1 REMARK 6 ABOVE). FURTHER, A MODEL IS AVAILABLE FOR DOCKING THE REMARK 6 DNA BINDING N-DOMAIN WITH THE RECA OPERATOR SITE (REF.2 REMARK 6 ABOVE) CONSISTENT WITH VARIOUS TYPES OF BIOCHEMICAL DATA REMARK 6 AND MONTE-CARLO CALCULATIONS. THE CRYSTAL STRUCTURE OF REMARK 6 REMARK 6 A RELATED SOS PROTEIN, UMUD' (PDB CODE 1UMU; REF. 3 REMARK 6 REMARK 6 ABOVE), SHARING 32% AMINO ACID IDENTITY WITH RESIDUES REMARK 6 85-202 OF LEXA HAS BEEN USED BY US TO GENERATE A MODEL REMARK 6 FOR THE C-DOMAIN OF LEXA. REMARK 6 REMARK 6 WE HAVE GENERATED A MODEL FOR THE LINKER REGION, IN REMARK 6 PARTICULAR, RESIDUES 70-105, CONTAINING THE AUTOCLEAVAGE REMARK 6 SITE AT ALA 84 - GLY 85, THAT CAN SATISFY THE ACCUMULATED REMARK 6 BIOCHEMICAL DATA (REFS. 4-11 AND MORE). THE RECA OPERATOR REMARK 6 DNA IS IN IDEAL B-DNA CONFORMATION IN OUR MODEL. REMARK 6 REMARK 6 IN THIS MODEL, THE SITE OF CLEAVAGE IS QUITE CLOSE TO REMARK 6 THE CATALYTIC SER 119 AND LYS 156, BUT CLEAVAGE DOES REMARK 6 NOT OCCUR AS THE ALA-GLY IS FURTHER THAN THE PROXIMITY REMARK 6 REQUIRED FOR AUTOCLEAVAGE. ONLY A SMALL STRUCTURAL REMARK 6 CHANGE, EITHER INDUCED BY ACTIVATED RECA OR ELEVATED PH REMARK 6 BRINGS THE SUBSTRATE CLOSER AND CLEAVAGE OCCURS. REMARK 6 REMARK 6 THE TWO LEXA MONOMERS BOUND TO THE RECA OPERATOR SITE REMARK 6 INTERACT WITH EACH OTHER MAINLY VIA THE C-DOMAINS. REMARK 6 A NEW BETA BARREL IS CREATED AS THE TWO C-DOMAINS REMARK 6 INTERACT, CONTAINING FOUR BETA STRANDS FROM EACH REMARK 6 MONOMER. THE INTERACTION IS DIFFERENT THAN FOUND IN REMARK 6 REMARK 6 THE CASE OF UMUD' DIMER IN THE CRYSTAL. REMARK 6 REMARK 6 REMARK 6 MODEL BUILDING FOR THE COMPLETE LEXA DIMER WAS CARRIED REMARK 6 OUT USING THE INSIGHT-II PACKAGE INCLUDING PROGRAMS REMARK 6 DISCOVER AND HOMOLOGY REMARK 7 REMARK 7 THERE ARE TWO COMPLETE LEXA MOLECULES WITH CHAIN REMARK 7 IDENTIFIERS *A* AND *B*. OPERATOR DNA CHAIN IDENTIFIERS REMARK 7 *C* AND *D*. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-1999. REMARK 100 THE RCSB ID CODE IS RCSB000408. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 C2* A D 2 NE2 HIS B 46 1.31 REMARK 500 C5M T D 4 CB ALA B 42 1.41 REMARK 500 N4 C D 3 OE1 GLU B 45 1.55 REMARK 500 O6 G D 5 ND2 ASN B 41 1.58 REMARK 500 C5M T C 4 CB ALA A 42 1.61 REMARK 500 O6 G C 5 ND2 ASN A 41 1.69 REMARK 500 O2P C D 3 CD2 HIS B 46 1.81 REMARK 500 C2* A D 2 CE1 HIS B 46 1.87 REMARK 500 C2* A C 2 NE2 HIS A 46 1.88 REMARK 500 C5M T D 4 CA ALA B 42 1.92 REMARK 500 O1P T C 4 CB ARG A 38 1.97 REMARK 500 O1P T C 4 NE ARG A 38 1.97 REMARK 500 O1P T D 4 CB ARG B 38 1.99 REMARK 500 O2P C D 3 NE2 HIS B 46 2.04 REMARK 500 O1P T C 4 CD ARG A 38 2.05 REMARK 500 O1P C D 3 NE ARG B 7 2.05 REMARK 500 O3* T D 1 OG1 THR B 5 2.06 REMARK 500 N6 A C 17 OE2 GLU B 45 2.07 REMARK 500 O2P A D 15 OE1 GLU A 44 2.07 REMARK 500 O1P C C 3 NE ARG A 7 2.10 REMARK 500 O3* A D 2 CG ARG B 7 2.12 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 GLN B 70 -59.35 72.65 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 77 LEU A 78 -149.07 REMARK 500 LYS A 106 PRO A 107 -130.10 REMARK 500 VAL A 178 VAL A 179 148.88 REMARK 500 VAL B 178 VAL B 179 144.48 DBREF 1QAA A 1 202 UNP P03033 LEXA_ECOLI 1 202 DBREF 1QAA B 1 202 UNP P03033 LEXA_ECOLI 1 202 SEQRES 1 C 20 T A C T G T A T G A G C A SEQRES 2 C 20 T A C A G T A SEQRES 1 D 20 T A C T G T A T G C T C A SEQRES 2 D 20 T A C A G T A SEQRES 1 A 202 MET LYS ALA LEU THR ALA ARG GLN GLN GLU VAL PHE ASP SEQRES 2 A 202 LEU ILE ARG ASP HIS ILE SER GLN THR GLY MET PRO PRO SEQRES 3 A 202 THR ARG ALA GLU ILE ALA GLN ARG LEU GLY PHE ARG SER SEQRES 4 A 202 PRO ASN ALA ALA GLU GLU HIS LEU LYS ALA LEU ALA ARG SEQRES 5 A 202 LYS GLY VAL ILE GLU ILE VAL SER GLY ALA SER ARG GLY SEQRES 6 A 202 ILE ARG LEU LEU GLN GLU GLU GLU GLU GLY LEU PRO LEU SEQRES 7 A 202 VAL GLY ARG VAL ALA ALA GLY GLU PRO LEU LEU ALA GLN SEQRES 8 A 202 GLN HIS ILE GLU GLY HIS TYR GLN VAL ASP PRO SER LEU SEQRES 9 A 202 PHE LYS PRO ASN ALA ASP PHE LEU LEU ARG VAL SER GLY SEQRES 10 A 202 MET SER MET LYS ASP ILE GLY ILE MET ASP GLY ASP LEU SEQRES 11 A 202 LEU ALA VAL HIS LYS THR GLN ASP VAL ARG ASN GLY GLN SEQRES 12 A 202 VAL VAL VAL ALA ARG ILE ASP ASP GLU VAL THR VAL LYS SEQRES 13 A 202 ARG LEU LYS LYS GLN GLY ASN LYS VAL GLU LEU LEU PRO SEQRES 14 A 202 GLU ASN SER GLU PHE LYS PRO ILE VAL VAL ASP LEU ARG SEQRES 15 A 202 GLN GLN SER PHE THR ILE GLU GLY LEU ALA VAL GLY VAL SEQRES 16 A 202 ILE ARG ASN GLY ASP TRP LEU SEQRES 1 B 202 MET LYS ALA LEU THR ALA ARG GLN GLN GLU VAL PHE ASP SEQRES 2 B 202 LEU ILE ARG ASP HIS ILE SER GLN THR GLY MET PRO PRO SEQRES 3 B 202 THR ARG ALA GLU ILE ALA GLN ARG LEU GLY PHE ARG SER SEQRES 4 B 202 PRO ASN ALA ALA GLU GLU HIS LEU LYS ALA LEU ALA ARG SEQRES 5 B 202 LYS GLY VAL ILE GLU ILE VAL SER GLY ALA SER ARG GLY SEQRES 6 B 202 ILE ARG LEU LEU GLN GLU GLU GLU GLU GLY LEU PRO LEU SEQRES 7 B 202 VAL GLY ARG VAL ALA ALA GLY GLU PRO LEU LEU ALA GLN SEQRES 8 B 202 GLN HIS ILE GLU GLY HIS TYR GLN VAL ASP PRO SER LEU SEQRES 9 B 202 PHE LYS PRO ASN ALA ASP PHE LEU LEU ARG VAL SER GLY SEQRES 10 B 202 MET SER MET LYS ASP ILE GLY ILE MET ASP GLY ASP LEU SEQRES 11 B 202 LEU ALA VAL HIS LYS THR GLN ASP VAL ARG ASN GLY GLN SEQRES 12 B 202 VAL VAL VAL ALA ARG ILE ASP ASP GLU VAL THR VAL LYS SEQRES 13 B 202 ARG LEU LYS LYS GLN GLY ASN LYS VAL GLU LEU LEU PRO SEQRES 14 B 202 GLU ASN SER GLU PHE LYS PRO ILE VAL VAL ASP LEU ARG SEQRES 15 B 202 GLN GLN SER PHE THR ILE GLU GLY LEU ALA VAL GLY VAL SEQRES 16 B 202 ILE ARG ASN GLY ASP TRP LEU HELIX 1 1 THR A 5 GLY A 23 1 19 HELIX 2 2 THR A 27 GLY A 36 1 10 HELIX 3 3 SER A 39 GLY A 54 1 16 HELIX 4 4 LEU A 88 HIS A 93 1 6 HELIX 5 5 MET A 120 GLY A 124 5 5 HELIX 6 6 THR B 5 GLY B 23 1 19 HELIX 7 7 THR B 27 GLY B 36 1 10 HELIX 8 8 SER B 39 GLY B 54 1 16 HELIX 9 9 LEU B 88 GLU B 95 1 8 HELIX 10 10 MET B 120 GLY B 124 5 5 SHEET 1 A 2 ILE A 56 ILE A 58 0 SHEET 2 A 2 ILE A 66 LEU A 68 -1 N ARG A 67 O GLU A 57 SHEET 1 B 7 ASP A 110 ARG A 114 0 SHEET 2 B 7 LEU A 130 HIS A 134 -1 N LEU A 131 O LEU A 113 SHEET 3 B 7 PHE A 186 ILE A 196 -1 O LEU A 191 N HIS A 134 SHEET 4 B 7 GLN A 143 ILE A 149 -1 O VAL A 144 N ALA A 192 SHEET 5 B 7 GLU A 152 LYS A 159 -1 N GLU A 152 O ILE A 149 SHEET 6 B 7 VAL A 165 LEU A 168 -1 O GLU A 166 N LYS A 159 SHEET 7 B 7 ILE A 177 VAL A 179 -1 O ILE A 177 N LEU A 167 SHEET 1 C 2 ILE B 56 ILE B 58 0 SHEET 2 C 2 ILE B 66 LEU B 68 -1 N ARG B 67 O GLU B 57 SHEET 1 D 7 ASP B 110 ARG B 114 0 SHEET 2 D 7 LEU B 130 HIS B 134 -1 N LEU B 131 O LEU B 113 SHEET 3 D 7 PHE B 186 ILE B 196 -1 O LEU B 191 N HIS B 134 SHEET 4 D 7 GLN B 143 ILE B 149 -1 O VAL B 144 N ALA B 192 SHEET 5 D 7 GLU B 152 LYS B 159 -1 N GLU B 152 O ILE B 149 SHEET 6 D 7 GLU B 166 LEU B 168 -1 O GLU B 166 N LYS B 159 SHEET 7 D 7 ILE B 177 VAL B 178 -1 O ILE B 177 N LEU B 167 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 MASTER 205 0 0 10 18 0 0 6 0 0 0 36 END