10 20 30 40 50 60 70 80 2JVB - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, KEYWDS 2 MANGANESE, METAL-BINDING, MRNA PROCESSING, NONSENSE- KEYWDS 3 MEDIATED MRNA DECAY, NUCLEUS, PHOSPHORYLATION, RNA-BINDING
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR M.DESHMUKH,J.GROSS
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, JRNL AUTH 2 S.N.FLOOR,C.KIM,J.JEMIELITY,M.KALEK, JRNL AUTH 3 E.DARZYNKIEWICZ,J.D.GROSS JRNL TITL MRNA DECAPPING IS PROMOTED BY AN RNA-BINDING JRNL TITL 2 CHANNEL IN 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 1
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 RCSB ID CODE IS RCSB100335.
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- REMARK 210 YDCP2, 90% H2O/10% D2O; 500 UM REMARK 210 [U-100% 13C] GB1-YDCP2, 90% REMARK 210 H2O/10% D2O; 500 UM [U-100% REMARK 210 13C, 1H ILV ONLY; U-100% 15N; REMARK 210 100% 2H] GB1-YDCP2, 90% H2O/ REMARK 210 10% D2O; 500 UM [U-100% 13C; U REMARK 210 -100% 15N; 80% 2H] GB1-YDCP2, REMARK 210 90% H2O/10% D2O; 500 UM [U- REMARK 210 100% 13C,1H METHYL GROUPS OF I REMARK 210 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 REMARK 210 HSQC, 2D 1H-1H TOCSY, 2D 1H-1H REMARK 210 NOESY, 3D C(CO)NH, 3D HNCO, 3D REMARK 210 HNCA, 3D HNCACB, 3D HN(CO)CA, REMARK 210 3D 1H-15N NOESY, 3D HN(COCA) REMARK 210 CB, 3D H(CCO)NH, 3D 13C EDITED REMARK 210 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 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: 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 9 VAL A 195 -166.43 -126.84 REMARK 500 9 ARG A 196 150.50 -46.84 REMARK 500 9 GLU A 198 -113.43 -171.37 REMARK 500 9 THR A 213 7.85 51.13 REMARK 500 10 ASN A 112 151.93 -47.23 REMARK 500 10 ASP A 139 38.15 77.70 REMARK 500 10 GLU A 153 -62.13 -91.61 REMARK 500 10 THR A 159 -61.52 -90.40 REMARK 500 10 ASN A 197 102.57 -56.99 REMARK 500 10 GLU A 198 -113.26 -155.36 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 REMARK 900 ASSIGNMENTS 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