HEADER NUCLEOTIDYLTRANSFERASE 12-APR-94 1BPB 1BPB 2 COMPND DNA POLYMERASE BETA (BETA POLYMERASE) (E.C.2.7.7.7) 1BPB 3 COMPND 2 (APO, 31KD DOMAIN) 1BPB 4 SOURCE RAT (RATTUS NORVEGICUS) RECOMBINANT FORM EXPRESSED IN 1BPBA 1 SOURCE 2 (ESCHERICHIA COLI) 1BPBA 2 AUTHOR M.R.SAWAYA,H.PELLETIER,A.KUMAR,S.H.WILSON,J.KRAUT 1BPB 6 REVDAT 2 15-OCT-94 1BPBA 1 SOURCE REMARK 1BPBA 3 REVDAT 1 22-JUN-94 1BPB 0 1BPB 7 REMARK 1 1BPB 8 REMARK 1 REFERENCE 1 1BPB 9 REMARK 1 AUTH M.R.SAWAYA,H.PELLETIER,A.KUMAR,S.H.WILSON,J.KRAUT 1BPB 10 REMARK 1 TITL CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: 1BPB 11 REMARK 1 TITL 2 EVIDENCE FOR A COMMON POLYMERASE MECHANISM 1BPBA 4 REMARK 1 REF SCIENCE V. 264 1930 1994 1BPBA 5 REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 0038 1BPBA 6 REMARK 1 REFERENCE 2 1BPB 15 REMARK 1 AUTH H.PELLETIER,M.R.SAWAYA,S.H.WILSON,J.KRAUT 1BPB 16 REMARK 1 TITL STRUCTURES OF TERNARY COMPLEXES OF RAT DNA 1BPBA 7 REMARK 1 TITL 2 POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP 1BPBA 8 REMARK 1 REF SCIENCE V. 264 1891 1994 1BPBA 9 REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 0038 1BPBA 10 REMARK 1 REFERENCE 3 1BPB 22 REMARK 1 AUTH A.KUMAR,S.G.WIDEN,K.R.WILLIAMS,P.KEDAR,R.L.KARPEL, 1BPB 23 REMARK 1 AUTH 2 S.H.WILSON 1BPB 24 REMARK 1 TITL STUDIES OF THE DOMAIN STRUCTURE OF MAMMALIAN DNA 1BPB 25 REMARK 1 TITL 2 POLYMERASE BETA. IDENTIFICATION OF A DISCRETE 1BPB 26 REMARK 1 TITL 3 TEMPLATE BINDING DOMAIN 1BPB 27 REMARK 1 REF J.BIOL.CHEM. V. 265 2124 1990 1BPB 28 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 0071 1BPB 29 REMARK 2 1BPB 30 REMARK 2 RESOLUTION. 2.3 ANGSTROMS. 1BPB 31 REMARK 3 1BPB 32 REMARK 3 REFINEMENT. 1BPB 33 REMARK 3 PROGRAM TNT 1BPB 34 REMARK 3 AUTHORS TRONRUD,TEN EYCK,MATTHEWS 1BPB 35 REMARK 3 R VALUE 0.193 1BPB 36 REMARK 3 RMSD BOND DISTANCES 0.023 ANGSTROMS 1BPB 37 REMARK 3 RMSD BOND ANGLES 3.0 DEGREES 1BPB 38 REMARK 3 1BPB 39 REMARK 3 NUMBER OF REFLECTIONS 13634 1BPB 40 REMARK 3 DATA CUTOFF 0.0 SIGMA(F) 1BPB 41 REMARK 3 PERCENT COMPLETION 93.1 1BPB 42 REMARK 3 1BPB 43 REMARK 3 NUMBER OF PROTEIN ATOMS 1934 1BPB 44 REMARK 3 NUMBER OF SOLVENT ATOMS 90 1BPB 45 REMARK 4 1BPB 46 REMARK 4 RESIDUES ASP 91, ASP 92, SER 109, ILE 119, GLU 123, LYS 1BPB 47 REMARK 4 131, LYS 206, LYS 220, SER 243, GLU 244, ASN 245, LYS 280, 1BPB 48 REMARK 4 VAL 303,THR 304, VAL 306, AND ARG 326 HAVE INCOMPLETE SIDE 1BPB 49 REMARK 4 CHAIN ATOMS. RESIDUES 246 - 248 ARE IN A DISORDERED LOOP 1BPBA 11 REMARK 4 AND ARE NOT INCLUDED IN THIS ENTRY. 1BPBA 12 REMARK 5 1BPBA 13 REMARK 5 DNA POLYMERASE BETA POSSESSES A PROTEOLYTICALLY SENSITIVE 1BPBA 14 REMARK 5 REGION IN ITS AMINO ACID SEQUENCE (RESIDUES 80 - 90), AND 1BPBA 15 REMARK 5 THE PRECISE CLEAVAGE SITE VARIES DEPENDING ON THE PROTEASE 1BPBA 16 REMARK 5 OR THE CHEMICAL REAGENT USED IN THE CLEAVAGE REACTION (SEE 1BPBA 17 REMARK 5 A. KUMAR ET AL., J. BIOL. CHEM. 265, 2124 (1990)). THE 1BPBA 18 REMARK 5 AUTHORS SUSPECT THAT A BACTERIAL PROTEASE OF UNKNOWN ORIGIN 1BPBA 19 REMARK 5 UNEXPECTEDLY CLEAVED THEIR INTACT ENZYME DURING THE 1BPBA 20 REMARK 5 CRYSTALLIZATION PROCESS, RESULTING IN CRYSTALS OF THE 1BPBA 21 REMARK 5 PROTEIN STRUCTURE REPORTED IN THIS ENTRY - THE 31-KD 1BPBA 22 REMARK 5 COOH-TERMINAL DOMAIN (RESIDUES 88 - 335) OF DNA POLYMERASE 1BPBA 23 REMARK 5 BETA. BECAUSE THE AUTHORS HAVE NOT DONE AN N-TERMINAL 1BPBA 24 REMARK 5 ANALYSIS ON THE PROTEIN IN THEIR CRYSTALS, THEIR CHOICE OF 1BPBA 25 REMARK 5 THE CLEAVAGE SITE (BETWEEN RESIDUES 87 AND 88) IS RATHER 1BPBA 26 REMARK 5 ARBITRARY, AND IN FACT, THERE MAY EVEN BE VARIABLE 1BPBA 27 REMARK 5 N-TERMINAL RESIDUES WITHIN ANY GIVEN CRYSTAL OF THIS 1BPBA 28 REMARK 5 CLEAVED PROTEIN. 1BPBA 29 REMARK 6 1BPBA 30 REMARK 6 PLEASE NOTE THAT THIS ENTRY IS ONLY THE 31 KD DOMAIN AND 1BPBA 31 REMARK 6 THE FIRST 8 KD DOMAIN IS NOT PRESENT IN THIS STRUCTURE. 1BPBA 32 REMARK 6 1BPB 62 REMARK 6 PDB ADVISORY NOTICE: 1BPB 63 REMARK 6 WATER MOLECULES 441, 468, AND 477 ARE VERY CLOSE TO SPECIAL 1BPB 64 REMARK 6 POSITIONS. 1BPB 65 REMARK 7 1BPB 66 REMARK 7 SEQUENCE ADVISORY NOTICE 1BPB 67 REMARK 7 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. 1BPB 68 REMARK 7 1BPB 69 REMARK 7 SWISS-PROT ENTRY NAME: DPOB_RAT 1BPB 70 REMARK 7 1BPB 71 REMARK 7 SWISS-PROT RESIDUE PDB SEQRES 1BPB 72 REMARK 7 1BPB 73 REMARK 7 NAME NUMBER NAME CHAIN SEQ/INSERT CODE 1BPB 74 REMARK 7 ARG 227 LEU 228 1BPB 75 REMARK 7 1BPB 76 REMARK 7 THE PAPER BY KUMAR, ET AL., J.BIOL.CHEM., 265, 2124, 1BPB 77 REMARK 7 (1990) REPORTS A CORRECTION TO THE SEQUENCE GIVEN IN 1BPB 78 REMARK 7 SWISS-PROT (SEE REFERENCE 3 ABOVE). 1BPB 79 REMARK 8 1BPBA 33 REMARK 8 PDB ADVISORY NOTICE: 1BPBA 34 REMARK 8 WATER MOLECULES 441, 468, AND 477 ARE VERY CLOSE TO SPECIAL 1BPBA 35 REMARK 8 POSITIONS. 1BPBA 36 REMARK 9 1BPBA 37 REMARK 9 CORRECTION. CORRECT SOURCE INFORMATION. UPDATE 1BPBA 38 REMARK 9 REFERENCES TO REFLECT PUBLICATION. REVISE AND REORDER 1BPBA 39 REMARK 9 REMARKS. 15-OCT-94. 1BPBA 40 SEQRES 1 248 ILE ARG GLN ASP ASP THR SER SER SER ILE ASN PHE LEU 1BPBA 41 SEQRES 2 248 THR ARG VAL THR GLY ILE GLY PRO SER ALA ALA ARG LYS 1BPBA 42 SEQRES 3 248 LEU VAL ASP GLU GLY ILE LYS THR LEU GLU ASP LEU ARG 1BPBA 43 SEQRES 4 248 LYS ASN GLU ASP LYS LEU ASN HIS HIS GLN ARG ILE GLY 1BPBA 44 SEQRES 5 248 LEU LYS TYR PHE GLU ASP PHE GLU LYS ARG ILE PRO ARG 1BPBA 45 SEQRES 6 248 GLU GLU MET LEU GLN MET GLN ASP ILE VAL LEU ASN GLU 1BPBA 46 SEQRES 7 248 VAL LYS LYS LEU ASP PRO GLU TYR ILE ALA THR VAL CYS 1BPBA 47 SEQRES 8 248 GLY SER PHE ARG ARG GLY ALA GLU SER SER GLY ASP MET 1BPBA 48 SEQRES 9 248 ASP VAL LEU LEU THR HIS PRO ASN PHE THR SER GLU SER 1BPBA 49 SEQRES 10 248 SER LYS GLN PRO LYS LEU LEU HIS ARG VAL VAL GLU GLN 1BPBA 50 SEQRES 11 248 LEU GLN LYS VAL ARG PHE ILE THR ASP THR LEU SER LYS 1BPBA 51 SEQRES 12 248 GLY GLU THR LYS PHE MET GLY VAL CYS GLN LEU PRO SER 1BPBA 52 SEQRES 13 248 GLU ASN ASP GLU ASN GLU TYR PRO HIS ARG ARG ILE ASP 1BPBA 53 SEQRES 14 248 ILE ARG LEU ILE PRO LYS ASP GLN TYR TYR CYS GLY VAL 1BPBA 54 SEQRES 15 248 LEU TYR PHE THR GLY SER ASP ILE PHE ASN LYS ASN MET 1BPBA 55 SEQRES 16 248 ARG ALA HIS ALA LEU GLU LYS GLY PHE THR ILE ASN GLU 1BPBA 56 SEQRES 17 248 TYR THR ILE ARG PRO LEU GLY VAL THR GLY VAL ALA GLY 1BPBA 57 SEQRES 18 248 GLU PRO LEU PRO VAL ASP SER GLU GLN ASP ILE PHE ASP 1BPBA 58 SEQRES 19 248 TYR ILE GLN TRP ARG TYR ARG GLU PRO LYS ASP ARG SER 1BPBA 59 SEQRES 20 248 GLU 1BPBA 60 FTNOTE 1 1BPB 106 FTNOTE 1 GLY 274 - SER 275 OMEGA =359.35 1BPB 107 FTNOTE 1 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 1BPB 108 FORMUL 2 HOH *90(H2 O1) 1BPB 109 CRYST1 120.576 63.520 38.215 90.00 90.00 90.00 P 21 21 2 4 1BPB 110 ORIGX1 1.000000 0.000000 0.000000 0.00000 1BPB 111 ORIGX2 0.000000 1.000000 0.000000 0.00000 1BPB 112 ORIGX3 0.000000 0.000000 1.000000 0.00000 1BPB 113 SCALE1 0.008294 0.000000 0.000000 0.00000 1BPB 114 SCALE2 0.000000 0.015743 0.000000 0.00000 1BPB 115 SCALE3 0.000000 0.000000 0.026168 0.00000 1BPB 116