HEADER METAL BINDING PROTEIN 23-FEB-10 2KUO TITLE STRUCTURE AND IDENTIFICATION OF ADP-RIBOSE RECOGNITION MOTIFS OF APLF TITLE 2 AND ROLE IN THE DNA DAMAGE RESPONSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: APRATAXIN AND PNK-LIKE FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APLF TZF; COMPND 5 SYNONYM: APURINIC-APYRIMIDINIC ENDONUCLEASE APLF, PNK AND APTX-LIKE COMPND 6 FHA DOMAIN-CONTAINING PROTEIN, XRCC1-INTERACTING PROTEIN 1; COMPND 7 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: APLF, APLF(C2ORF13), C2ORF13, PALF, XIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T KEYWDS APRATAXIN PNK-LIKE FACTOR (APLF), POLY ADP-RIBOSE (PAR), PAR-BINDING KEYWDS 2 ZINC FINGER (PBZ), DNA DAMAGE, ADP-RIBOSE, ADP-RIBOSYLATION, DNA KEYWDS 3 REPAIR, METAL-BINDING, NUCLEOTIDE-BINDING, NUCLEUS, ZINC, ZINC- KEYWDS 4 FINGER, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.Y.LI,R.D.MCCULLOCH,A.FENTON,M.CHEUNG,L.MENG,M.IKURA,C.A.KOCH REVDAT 2 16-MAR-22 2KUO 1 REMARK SEQADV REVDAT 1 05-MAY-10 2KUO 0 JRNL AUTH G.Y.LI,R.D.MCCULLOCH,A.FENTON,M.CHEUNG,L.MENG,M.IKURA, JRNL AUTH 2 C.A.KOCH JRNL TITL STRUCTURE AND IDENTIFICATION OF ADP-RIBOSE RECOGNITION JRNL TITL 2 MOTIFS OF APRATAXIN PNK-LIKE FACTOR (APLF) REQUIRED FOR THE JRNL TITL 3 INTERACTION WITH SITES OF DNA DAMAGE RESPONSE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS 1.1 REMARK 3 AUTHORS : GUNTERT, P. ET AL. (CYANA), BRUNGER, A. ET AL. REMARK 3 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA, CNS REMARK 4 REMARK 4 2KUO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000101594. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298 REMARK 210 PH : 6.0; 7.4; 6.0 REMARK 210 IONIC STRENGTH : 50; 150; 500 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-0.8 MM [U-100% 13C; U-100% REMARK 210 15N] APLF TANDEM ZF, 20 MM BIS- REMARK 210 TRIS, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM SODIUM AZIDE, 0.05 MM ZINC REMARK 210 CHLORIDE, 93% H2O/7% D2O; 0.5- REMARK 210 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 APLF TANDEM ZF, 20 MM BIS-TRIS, REMARK 210 50 MM SODIUM CHLORIDE, 1 MM REMARK 210 SODIUM AZIDE, 0.05 MM ZINC REMARK 210 CHLORIDE, 99% D2O; 0.1 MM [U-100% REMARK 210 15N] APLF TANDEM ZF, 20 MM BIS- REMARK 210 TRIS, 50 MM SODIUM CHLORIDE, 1 REMARK 210 MM SODIUM AZIDE, 0.05 MM ZINC REMARK 210 CHLORIDE, 93% H2O/7% D2O; 0.1 MM REMARK 210 [U-100% 15N] APLF TANDEM ZF, 20 REMARK 210 MM SODIUM PHOSPHATE, 150 MM REMARK 210 POTASSIUM CHLORIDE, 1 MM SODIUM REMARK 210 AZIDE, 0.05 MM ZINC CHLORIDE, 2 REMARK 210 MM MAGNESIUM CHLORIDE, 93% H2O/7% REMARK 210 D2O; 0.5 MM [U-100% 15N] APLF REMARK 210 TANDEM ZF, 20 MM BIS-TRIS, 500 REMARK 210 MM SODIUM CHLORIDE, 1 MM SODIUM REMARK 210 AZIDE, 0.05 MM ZINC CHLORIDE, 10 REMARK 210 MG/ML PF1 PHAGE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 2D 1H- REMARK 210 15N IPAP HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MOLMOL 2K, NMRPIPE, TALOS, REMARK 210 TOPSPIN, XEASY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 DISTANCE 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 LYS A 360 92.09 -67.85 REMARK 500 1 GLU A 370 31.35 -95.63 REMARK 500 1 CYS A 379 103.02 -54.18 REMARK 500 1 PRO A 399 93.12 -59.34 REMARK 500 1 ASP A 413 141.56 174.56 REMARK 500 1 ASP A 416 -64.96 68.27 REMARK 500 1 ASP A 417 -25.15 -156.50 REMARK 500 1 VAL A 445 27.73 41.85 REMARK 500 1 ASN A 447 79.76 -116.03 REMARK 500 2 LYS A 360 110.65 -162.94 REMARK 500 2 GLN A 367 99.11 -60.60 REMARK 500 2 SER A 369 19.91 -146.11 REMARK 500 2 PRO A 399 -2.56 -54.74 REMARK 500 2 ASP A 417 79.04 78.07 REMARK 500 2 ASN A 431 127.75 -178.36 REMARK 500 3 PRO A 399 107.90 -51.07 REMARK 500 3 ASP A 413 114.46 -167.91 REMARK 500 3 THR A 415 -74.05 -101.18 REMARK 500 3 ASP A 416 -56.33 -179.72 REMARK 500 3 ASP A 417 -32.34 -175.15 REMARK 500 3 LYS A 430 94.18 -66.12 REMARK 500 3 ASN A 431 114.13 -173.57 REMARK 500 3 ASN A 447 85.84 52.98 REMARK 500 4 VAL A 365 80.46 -68.91 REMARK 500 4 PRO A 399 100.53 -52.96 REMARK 500 4 VAL A 410 90.06 -66.13 REMARK 500 4 ASP A 413 141.10 -170.49 REMARK 500 4 ASP A 416 -31.80 179.44 REMARK 500 4 ASP A 417 79.75 63.17 REMARK 500 4 ASN A 431 126.37 -173.02 REMARK 500 4 VAL A 445 7.62 56.53 REMARK 500 4 ASN A 447 -36.59 -133.05 REMARK 500 5 VAL A 410 86.31 -66.33 REMARK 500 5 ASP A 413 121.58 -173.13 REMARK 500 5 THR A 415 -86.12 -65.50 REMARK 500 5 ASP A 416 -68.87 168.68 REMARK 500 5 ASN A 431 112.08 -163.23 REMARK 500 6 ALA A 361 80.08 -69.74 REMARK 500 6 GLN A 367 -4.99 55.95 REMARK 500 6 LYS A 373 -60.43 -90.49 REMARK 500 6 PRO A 399 104.98 -51.58 REMARK 500 6 ASP A 413 136.43 179.83 REMARK 500 6 THR A 415 -81.18 -87.80 REMARK 500 6 ASP A 416 -52.72 169.94 REMARK 500 6 ASP A 417 -31.73 -169.92 REMARK 500 6 VAL A 445 29.19 44.45 REMARK 500 6 ASN A 447 -76.21 47.92 REMARK 500 7 ALA A 361 97.51 -54.54 REMARK 500 7 GLN A 367 -68.43 67.81 REMARK 500 7 GLU A 370 41.32 -92.01 REMARK 500 REMARK 500 THIS ENTRY HAS 138 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 449 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 379 SG REMARK 620 2 CYS A 385 SG 116.0 REMARK 620 3 HIS A 392 NE2 107.9 103.6 REMARK 620 4 HIS A 398 NE2 103.5 119.9 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 450 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 421 SG REMARK 620 2 CYS A 427 SG 104.6 REMARK 620 3 HIS A 434 NE2 102.3 107.5 REMARK 620 4 HIS A 440 NE2 97.9 131.8 108.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 449 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 450 DBREF 2KUO A 360 448 UNP Q8IW19 APLF_HUMAN 360 448 SEQADV 2KUO GLY A -2 UNP Q8IW19 EXPRESSION TAG SEQADV 2KUO SER A -1 UNP Q8IW19 EXPRESSION TAG SEQRES 1 A 91 GLY SER LYS ALA THR ASP SER VAL LEU GLN GLY SER GLU SEQRES 2 A 91 GLY ASN LYS VAL LYS ARG THR SER CYS MET TYR GLY ALA SEQRES 3 A 91 ASN CYS TYR ARG LYS ASN PRO VAL HIS PHE GLN HIS PHE SEQRES 4 A 91 SER HIS PRO GLY ASP SER ASP TYR GLY GLY VAL GLN ILE SEQRES 5 A 91 VAL GLY GLN ASP GLU THR ASP ASP ARG PRO GLU CYS PRO SEQRES 6 A 91 TYR GLY PRO SER CYS TYR ARG LYS ASN PRO GLN HIS LYS SEQRES 7 A 91 ILE GLU TYR ARG HIS ASN THR LEU PRO VAL ARG ASN VAL HET ZN A 449 1 HET ZN A 450 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ASN A 389 HIS A 395 1 7 HELIX 2 2 ASN A 431 TYR A 438 1 8 SHEET 1 A 2 THR A 377 SER A 378 0 SHEET 2 A 2 PHE A 396 SER A 397 1 O SER A 397 N THR A 377 SHEET 1 B 2 PRO A 419 GLU A 420 0 SHEET 2 B 2 TYR A 438 ARG A 439 1 LINK SG CYS A 379 ZN ZN A 449 1555 1555 1.79 LINK SG CYS A 385 ZN ZN A 449 1555 1555 1.67 LINK NE2 HIS A 392 ZN ZN A 449 1555 1555 1.68 LINK NE2 HIS A 398 ZN ZN A 449 1555 1555 1.64 LINK SG CYS A 421 ZN ZN A 450 1555 1555 1.76 LINK SG CYS A 427 ZN ZN A 450 1555 1555 1.72 LINK NE2 HIS A 434 ZN ZN A 450 1555 1555 1.66 LINK NE2 HIS A 440 ZN ZN A 450 1555 1555 1.74 SITE 1 AC1 5 CYS A 379 GLY A 382 CYS A 385 HIS A 392 SITE 2 AC1 5 HIS A 398 SITE 1 AC2 4 CYS A 421 CYS A 427 HIS A 434 HIS A 440 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