HEADER PROTEIN BINDING 01-JUL-10 2L0F TITLE SOLUTION NMR STRUCTURE OF HUMAN POLYMERASE IOTA UBM2 (P692A MUTANT) IN TITLE 2 COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA POLYMERASE IOTA; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTEV; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS TRANSLESION DNA SYNTHESIS, DNA POLYMERASE IOTA, UBIQUITIN-BINDING KEYWDS 2 MOTIF, ISOPEPTIDE BOND, NUCLEUS, PHOSPHOPROTEIN, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,R.BENIRSCHKE,G.MER REVDAT 4 01-MAY-24 2L0F 1 REMARK SEQADV REVDAT 3 08-DEC-10 2L0F 1 JRNL REVDAT 2 01-DEC-10 2L0F 1 JRNL REVDAT 1 03-NOV-10 2L0F 0 JRNL AUTH G.CUI,R.C.BENIRSCHKE,H.F.TUAN,N.JURANIC,S.MACURA, JRNL AUTH 2 M.V.BOTUYAN,G.MER JRNL TITL STRUCTURAL BASIS OF UBIQUITIN RECOGNITION BY TRANSLESION JRNL TITL 2 SYNTHESIS DNA POLYMERASE IOTA. JRNL REF BIOCHEMISTRY V. 49 10198 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 21049971 JRNL DOI 10.1021/BI101303T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER 8 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000101799. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.18 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 UBM2, 3 MM UBIQUITIN, 20 MM REMARK 210 SODIUM PHOSPHATE, 30 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 5 MM REMARK 210 UBM2, 1.5 MM [U-100% 13C; U-100% REMARK 210 15N] UBIQUITIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 30 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] UBM2, 3 MM REMARK 210 UBIQUITIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 30 MM SODIUM CHLORIDE, REMARK 210 100% D2O; 5 MM UBM2, 1.5 MM [U- REMARK 210 100% 13C; U-100% 15N] UBIQUITIN, REMARK 210 20 MM SODIUM PHOSPHATE, 30 MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D HN(CA)CO; 3D H(CCO) REMARK 210 NH; 3D C(CO)NH; 3D 1H-15N TOCSY; REMARK 210 3D 15N, 13C FILTERED 13C EDITED REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SANE, NMRVIEW 5, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 4 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 5 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 12 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 13 ARG B 705 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 20 ARG A 74 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLN A 62 -166.82 -122.64 REMARK 500 1 LEU A 73 16.80 58.63 REMARK 500 1 ARG A 74 58.00 20.73 REMARK 500 1 LYS B 676 54.66 -152.91 REMARK 500 1 SER B 681 21.18 -63.74 REMARK 500 1 ASP B 709 15.85 54.82 REMARK 500 1 PHE B 710 -64.66 56.80 REMARK 500 1 HIS B 711 57.05 -177.08 REMARK 500 2 ASN A 60 19.47 59.98 REMARK 500 2 GLN A 62 -165.89 -120.79 REMARK 500 2 ARG A 74 54.66 31.95 REMARK 500 2 LYS B 676 53.67 -140.64 REMARK 500 2 SER B 681 20.48 -64.70 REMARK 500 2 ASP B 709 17.70 53.03 REMARK 500 2 PHE B 710 -69.19 59.05 REMARK 500 2 HIS B 711 65.22 178.72 REMARK 500 3 GLN A 62 -166.55 -127.83 REMARK 500 3 GLU B 675 82.95 59.07 REMARK 500 3 SER B 681 9.61 -62.23 REMARK 500 3 ASP B 709 17.00 52.36 REMARK 500 3 PHE B 710 -69.84 56.63 REMARK 500 3 HIS B 711 57.61 -175.41 REMARK 500 4 GLN A 62 -164.92 -121.89 REMARK 500 4 HIS B -2 -170.38 56.45 REMARK 500 4 LYS B 676 49.46 -143.06 REMARK 500 4 SER B 681 18.84 -63.48 REMARK 500 4 ASP B 709 18.33 52.84 REMARK 500 4 PHE B 710 -70.14 59.56 REMARK 500 4 HIS B 711 74.39 177.96 REMARK 500 5 GLN A 62 -169.70 -127.50 REMARK 500 5 ARG A 74 55.25 30.18 REMARK 500 5 MET B -1 -35.92 -146.40 REMARK 500 5 LYS B 676 39.08 -146.53 REMARK 500 5 SER B 681 20.61 -63.61 REMARK 500 5 ASP B 709 13.22 54.47 REMARK 500 5 PHE B 710 -74.66 51.28 REMARK 500 5 HIS B 711 47.75 -151.36 REMARK 500 6 GLN A 62 -165.61 -126.88 REMARK 500 6 GLU B 675 -98.84 -123.54 REMARK 500 6 LYS B 676 69.58 37.27 REMARK 500 6 SER B 681 4.68 -61.14 REMARK 500 6 ASP B 709 11.63 55.31 REMARK 500 6 PHE B 710 -70.18 57.60 REMARK 500 6 HIS B 711 57.05 -175.97 REMARK 500 7 ASN A 60 19.59 58.17 REMARK 500 7 GLN A 62 -166.05 -119.78 REMARK 500 7 LYS B 676 31.18 -77.56 REMARK 500 7 SER B 681 20.14 -64.80 REMARK 500 7 ASP B 709 12.50 56.91 REMARK 500 7 PHE B 710 -70.17 57.26 REMARK 500 REMARK 500 THIS ENTRY HAS 135 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 5 ARG A 42 0.08 SIDE CHAIN REMARK 500 9 ARG A 54 0.08 SIDE CHAIN REMARK 500 18 ARG A 42 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L0G RELATED DB: PDB DBREF 2L0F A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2L0F B 674 715 UNP Q9UNA4 POLI_HUMAN 674 715 SEQADV 2L0F GLY B -3 UNP Q9UNA4 EXPRESSION TAG SEQADV 2L0F HIS B -2 UNP Q9UNA4 EXPRESSION TAG SEQADV 2L0F MET B -1 UNP Q9UNA4 EXPRESSION TAG SEQADV 2L0F ALA B 692 UNP Q9UNA4 PRO 692 ENGINEERED MUTATION SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 45 GLY HIS MET ASP GLU LYS ILE THR PHE PRO SER ASP ILE SEQRES 2 B 45 ASP PRO GLN VAL PHE TYR GLU LEU ALA GLU ALA VAL GLN SEQRES 3 B 45 LYS GLU LEU LEU ALA GLU TRP LYS ARG THR GLY SER ASP SEQRES 4 B 45 PHE HIS ILE GLY HIS LYS HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 4 ASP B 684 LEU B 691 1 8 HELIX 5 5 ALA B 692 GLY B 707 1 16 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 SER A 65 LEU A 71 1 O SER A 65 N PHE A 4 SHEET 4 A 5 GLN A 41 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 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