HEADER HYDROLASE 16-SEP-07 2JVB TITLE SOLUTION STRUCTURE OF CATALYTIC DOMAIN OF YDCP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRNA-DECAPPING ENZYME SUBUNIT 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN PSU1; COMPND 5 EC: 3.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: DCP2, PSU1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS DCP2, MRNA DECAY, DECAPPING, CYTOPLASM, HYDROLASE, MANGANESE, METAL- KEYWDS 2 BINDING, MRNA PROCESSING, NONSENSE-MEDIATED MRNA DECAY, NUCLEUS, KEYWDS 3 PHOSPHORYLATION, RNA-BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.DESHMUKH,J.GROSS REVDAT 3 16-MAR-22 2JVB 1 REMARK REVDAT 2 24-FEB-09 2JVB 1 VERSN REVDAT 1 04-MAR-08 2JVB 0 JRNL AUTH M.V.DESHMUKH,B.N.JONES,D.U.QUANG-DANG,J.FLINDERS,S.N.FLOOR, JRNL AUTH 2 C.KIM,J.JEMIELITY,M.KALEK,E.DARZYNKIEWICZ,J.D.GROSS JRNL TITL MRNA DECAPPING IS PROMOTED BY AN RNA-BINDING CHANNEL IN JRNL TITL 2 DCP2. JRNL REF MOL.CELL V. 29 324 2008 JRNL REFN ISSN 1097-2765 JRNL PMID 18280238 JRNL DOI 10.1016/J.MOLCEL.2007.11.027 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, A.T. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JVB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100335. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 500 UM [U-100% 15N] GB1-YDCP2, REMARK 210 90% H2O/10% D2O; 500 UM [U-100% REMARK 210 13C] GB1-YDCP2, 90% H2O/10% D2O; REMARK 210 500 UM [U-100% 13C, 1H ILV ONLY; REMARK 210 U-100% 15N; 100% 2H] GB1-YDCP2, REMARK 210 90% H2O/10% D2O; 500 UM [U-100% REMARK 210 13C; U-100% 15N; 80% 2H] GB1- REMARK 210 YDCP2, 90% H2O/10% D2O; 500 UM REMARK 210 [U-100% 13C,1H METHYL GROUPS OF REMARK 210 I L AND V; 100% 2H] GB1-YDCP2, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D C(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HN(CO)CA; 3D 1H-15N REMARK 210 NOESY; 3D HN(COCA)CB; 3D H(CCO) REMARK 210 NH; 3D 13C EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-10 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASP A 245 O 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 HD22 ASN A 112 H SER A 116 1.29 REMARK 500 OD1 ASP A 164 H ASN A 165 1.53 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 ASN A 112 172.68 -58.64 REMARK 500 1 SER A 126 -102.68 -72.81 REMARK 500 1 THR A 159 -61.61 -90.22 REMARK 500 1 VAL A 195 -165.00 -129.15 REMARK 500 1 ARG A 196 152.61 -45.58 REMARK 500 1 GLU A 198 -113.65 -161.87 REMARK 500 1 TYR A 215 22.71 -72.17 REMARK 500 1 ASN A 218 -102.46 -137.02 REMARK 500 2 GLU A 125 -176.76 -55.33 REMARK 500 2 SER A 126 -76.85 -85.21 REMARK 500 2 ASP A 127 75.82 -109.54 REMARK 500 2 THR A 159 -61.70 -90.67 REMARK 500 2 GLU A 198 -112.85 -172.53 REMARK 500 2 TYR A 215 8.77 -67.70 REMARK 500 2 SER A 217 -44.75 -132.29 REMARK 500 2 ASN A 218 -39.56 -144.20 REMARK 500 2 ARG A 239 -15.89 -47.24 REMARK 500 3 SER A 126 -84.60 -68.23 REMARK 500 3 ASP A 127 69.29 -113.12 REMARK 500 3 THR A 159 -62.02 -91.07 REMARK 500 3 PRO A 193 116.13 -38.34 REMARK 500 3 ASN A 197 105.72 -54.90 REMARK 500 3 GLU A 198 -113.70 -171.97 REMARK 500 3 THR A 213 56.69 -66.02 REMARK 500 3 MET A 214 -72.80 -95.51 REMARK 500 4 LYS A 101 50.12 -140.70 REMARK 500 4 GLU A 125 -172.04 -54.94 REMARK 500 4 SER A 126 -120.93 -86.04 REMARK 500 4 GLU A 198 -113.34 -157.89 REMARK 500 4 LYS A 212 20.24 -73.29 REMARK 500 4 ASN A 218 16.36 -163.59 REMARK 500 4 TYR A 222 -73.52 -100.26 REMARK 500 5 GLU A 125 157.53 -47.02 REMARK 500 5 SER A 126 -70.03 -69.18 REMARK 500 5 ASN A 197 102.56 -46.21 REMARK 500 5 GLU A 198 -113.14 -147.30 REMARK 500 5 GLU A 244 -120.66 48.07 REMARK 500 6 LYS A 101 79.90 -108.65 REMARK 500 6 VAL A 195 -138.98 -130.23 REMARK 500 6 GLU A 198 -113.53 -150.61 REMARK 500 6 TYR A 222 -72.52 -101.49 REMARK 500 7 LYS A 101 48.46 -146.96 REMARK 500 7 GLU A 125 151.95 -43.52 REMARK 500 7 SER A 126 -83.36 -61.46 REMARK 500 7 THR A 159 -61.73 -90.31 REMARK 500 7 ASN A 197 102.01 -46.25 REMARK 500 7 GLU A 198 -113.45 -150.81 REMARK 500 8 GLU A 125 156.87 -47.39 REMARK 500 8 GLU A 198 -111.45 -172.65 REMARK 500 9 THR A 159 -61.70 -90.47 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7325 RELATED DB: BMRB REMARK 900 BACKBONE AND ILE(D1), LEU AND VAL SIDECHAIN RESONANCE ASSIGNMENTS REMARK 900 OF THE NUDIX DOMAIN OF YEAST DCP2 DBREF 2JVB A 100 245 UNP P53550 DCP2_YEAST 100 245 SEQRES 1 A 146 LYS LYS SER ILE PRO VAL ARG GLY ALA ALA ILE PHE ASN SEQRES 2 A 146 GLU ASN LEU SER LYS ILE LEU LEU VAL GLN GLY THR GLU SEQRES 3 A 146 SER ASP SER TRP SER PHE PRO ARG GLY LYS ILE SER LYS SEQRES 4 A 146 ASP GLU ASN ASP ILE ASP CYS CYS ILE ARG GLU VAL LYS SEQRES 5 A 146 GLU GLU ILE GLY PHE ASP LEU THR ASP TYR ILE ASP ASP SEQRES 6 A 146 ASN GLN PHE ILE GLU ARG ASN ILE GLN GLY LYS ASN TYR SEQRES 7 A 146 LYS ILE PHE LEU ILE SER GLY VAL SER GLU VAL PHE ASN SEQRES 8 A 146 PHE LYS PRO GLN VAL ARG ASN GLU ILE ASP LYS ILE GLU SEQRES 9 A 146 TRP PHE ASP PHE LYS LYS ILE SER LYS THR MET TYR LYS SEQRES 10 A 146 SER ASN ILE LYS TYR TYR LEU ILE ASN SER MET MET ARG SEQRES 11 A 146 PRO LEU SER MET TRP LEU ARG HIS GLN ARG GLN ILE LYS SEQRES 12 A 146 ASN GLU ASP HELIX 1 1 ASN A 141 ILE A 154 1 14 HELIX 2 2 PHE A 207 LYS A 212 1 6 HELIX 3 3 THR A 213 LYS A 216 5 4 HELIX 4 4 TYR A 221 LYS A 242 1 22 SHEET 1 A 4 ARG A 133 GLY A 134 0 SHEET 2 A 4 ARG A 106 ILE A 110 -1 N ARG A 106 O GLY A 134 SHEET 3 A 4 LYS A 175 ILE A 182 1 O LYS A 178 N GLY A 107 SHEET 4 A 4 PHE A 167 ILE A 172 -1 N ILE A 172 O LYS A 175 SHEET 1 B 2 LYS A 117 VAL A 121 0 SHEET 2 B 2 ILE A 202 ASP A 206 -1 O PHE A 205 N ILE A 118 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