HEADER LIGASE 03-OCT-12 2LZJ TITLE REFINED SOLUTION STRUCTURE AND DYNAMICS OF FIRST CATALYTIC CYSTEINE TITLE 2 HALF-DOMAIN FROM MOUSE E1 ENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIRST CATALYTIC CYSTEINE HALF-DOMAIN; COMPND 5 SYNONYM: UBIQUITIN-ACTIVATING ENZYME E1, UBIQUITIN-ACTIVATING ENZYME COMPND 6 E1 X, UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME 1 X; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: UBA1, SBX, UBE1, UBE1AX, UBE1X; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRS416 AND PRS413 KEYWDS CATALYTIC HALF-DOMAIN, MOUSE E1 ENZYME, BETA-BARREL ARCHITECTURE, KEYWDS 2 FLEXIBLE THERMINI, UBIQUITINYLATION, PROTEIN DEGRADATION, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.JAREMKO,L.JAREMKO,M.NOWAKOWSKI,R.H.SZCZEPANOWSKI,R.FILIPEK, AUTHOR 2 M.WOJCIECHOWSKI,M.BOCHTLER,A.EJCHART REVDAT 4 14-JUN-23 2LZJ 1 REMARK SEQADV REVDAT 3 08-JAN-14 2LZJ 1 JRNL REVDAT 2 04-DEC-13 2LZJ 1 JRNL REVDAT 1 18-SEP-13 2LZJ 0 JRNL AUTH M.JAREMKO,L.JAREMKO,M.NOWAKOWSKI,M.WOJCIECHOWSKI, JRNL AUTH 2 R.H.SZCZEPANOWSKI,R.PANECKA,I.ZHUKOV,M.BOCHTLER,A.EJCHART JRNL TITL NMR STRUCTURAL STUDIES OF THE FIRST CATALYTIC HALF-DOMAIN OF JRNL TITL 2 UBIQUITIN ACTIVATING ENZYME. JRNL REF J.STRUCT.BIOL. V. 185 69 2014 JRNL REFN ISSN 1047-8477 JRNL PMID 24211821 JRNL DOI 10.1016/J.JSB.2013.10.020 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.26, X-PLOR NIH 2.26 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000103021. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 FIRST CYSTEINE CATALYTIC HALF- REMARK 210 DOMAIN, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 15N] FIRST CYSTEINE REMARK 210 CATALYTIC HALF-DOMAIN, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HNHA; 3D HBHA(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D HN(CO)CA; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 400 MHZ; 700 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 OG SER A 302 HZ2 LYS A 304 1.29 REMARK 500 O VAL A 297 HZ1 LYS A 299 1.32 REMARK 500 O THR A 225 HG1 THR A 280 1.34 REMARK 500 HG SER A 218 OG SER A 293 1.38 REMARK 500 HE2 HIS A 240 O PRO A 272 1.38 REMARK 500 O SER A 222 HH TYR A 286 1.39 REMARK 500 HG1 THR A 225 O VAL A 231 1.39 REMARK 500 OD2 ASP A 246 HZ1 LYS A 296 1.39 REMARK 500 OE2 GLU A 266 HZ2 LYS A 268 1.39 REMARK 500 O PHE A 247 H VAL A 295 1.41 REMARK 500 OE2 GLU A 243 HZ3 LYS A 296 1.42 REMARK 500 HZ1 LYS A 226 OD1 ASP A 285 1.44 REMARK 500 H ASP A 227 OG1 THR A 280 1.49 REMARK 500 O LEU A 217 HG SER A 293 1.50 REMARK 500 O ASP A 236 HH TYR A 273 1.53 REMARK 500 O PHE A 202 H MET A 206 1.54 REMARK 500 O ASN A 212 H GLU A 214 1.55 REMARK 500 O GLY A 213 HE21 GLN A 215 1.56 REMARK 500 O GLU A 237 H ARG A 239 1.57 REMARK 500 H1 GLU A 201 OE1 GLU A 204 1.57 REMARK 500 OD1 ASP A 279 HG SER A 281 1.58 REMARK 500 OD1 ASP A 227 H ASN A 228 1.59 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 PHE A 202 -33.10 65.02 REMARK 500 1 THR A 209 34.39 -74.58 REMARK 500 1 SER A 211 94.17 -60.60 REMARK 500 1 ALA A 238 61.25 -65.83 REMARK 500 1 ARG A 239 85.09 -67.78 REMARK 500 1 CYS A 278 -96.25 -17.78 REMARK 500 1 PHE A 283 -76.52 -100.98 REMARK 500 1 SER A 284 -175.06 166.48 REMARK 500 1 ILE A 287 -69.15 -100.75 REMARK 500 1 ILE A 301 108.56 -49.68 REMARK 500 1 SER A 305 92.62 -53.06 REMARK 500 1 ALA A 308 120.48 -27.91 REMARK 500 2 PHE A 202 -29.17 63.31 REMARK 500 2 SER A 222 -71.51 -82.44 REMARK 500 2 CYS A 278 -94.76 -27.20 REMARK 500 2 PHE A 283 -83.08 -90.66 REMARK 500 2 SER A 284 -174.00 169.25 REMARK 500 2 ILE A 287 -64.06 -106.64 REMARK 500 3 PHE A 202 -47.80 56.46 REMARK 500 3 GLU A 252 18.47 59.17 REMARK 500 3 CYS A 278 -85.02 -22.05 REMARK 500 3 PHE A 283 -77.01 -92.25 REMARK 500 3 SER A 284 -179.30 169.23 REMARK 500 3 ILE A 287 -63.11 -100.17 REMARK 500 3 ARG A 288 -173.20 -172.41 REMARK 500 3 LYS A 296 97.02 -69.22 REMARK 500 3 LYS A 304 106.87 -50.06 REMARK 500 3 PRO A 307 47.70 -71.12 REMARK 500 3 ALA A 308 96.72 -28.65 REMARK 500 4 THR A 209 -72.04 -107.35 REMARK 500 4 PRO A 216 74.36 -59.89 REMARK 500 4 MET A 256 49.93 -81.24 REMARK 500 4 CYS A 278 -92.15 -29.73 REMARK 500 4 PHE A 283 -68.38 -94.96 REMARK 500 4 SER A 284 -87.93 164.39 REMARK 500 4 ARG A 288 173.09 173.45 REMARK 500 4 ALA A 308 74.73 -59.45 REMARK 500 5 PHE A 202 -58.04 47.91 REMARK 500 5 LEU A 208 70.32 -59.64 REMARK 500 5 SER A 222 -70.58 -77.98 REMARK 500 5 ARG A 239 99.09 -62.66 REMARK 500 5 CYS A 278 -88.88 -40.10 REMARK 500 5 PHE A 283 -80.74 -85.20 REMARK 500 5 SER A 284 -173.37 175.45 REMARK 500 5 ILE A 287 -74.78 -118.71 REMARK 500 5 ALA A 308 60.01 -110.16 REMARK 500 6 SER A 222 -68.52 -97.16 REMARK 500 6 GLU A 252 27.36 48.59 REMARK 500 6 CYS A 278 -78.77 -48.95 REMARK 500 6 PHE A 283 -74.78 -83.76 REMARK 500 REMARK 500 THIS ENTRY HAS 175 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Z7L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF FRAGMENT OF MOUSE UBIQUITIN-ACTIVATING ENZYME REMARK 900 RELATED ID: 3CMM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UBA1-UBIQUITIN COMPLEX REMARK 900 RELATED ID: 18758 RELATED DB: BMRB DBREF 2LZJ A 202 312 UNP Q02053 UBA1_MOUSE 202 312 SEQADV 2LZJ GLU A 201 UNP Q02053 EXPRESSION TAG SEQRES 1 A 112 GLU PHE GLY GLU GLU MET VAL LEU THR ASP SER ASN GLY SEQRES 2 A 112 GLU GLN PRO LEU SER ALA MET VAL SER MET VAL THR LYS SEQRES 3 A 112 ASP ASN PRO GLY VAL VAL THR CYS LEU ASP GLU ALA ARG SEQRES 4 A 112 HIS GLY PHE GLU THR GLY ASP PHE VAL SER PHE SER GLU SEQRES 5 A 112 VAL GLN GLY MET ILE GLN LEU ASN GLY CYS GLN PRO MET SEQRES 6 A 112 GLU ILE LYS VAL LEU GLY PRO TYR THR PHE SER ILE CYS SEQRES 7 A 112 ASP THR SER ASN PHE SER ASP TYR ILE ARG GLY GLY ILE SEQRES 8 A 112 VAL SER GLN VAL LYS VAL PRO LYS LYS ILE SER PHE LYS SEQRES 9 A 112 SER LEU PRO ALA SER LEU VAL GLU HELIX 1 1 MET A 256 GLY A 261 1 6 HELIX 2 2 ASP A 279 PHE A 283 5 5 SHEET 1 A 7 SER A 218 THR A 225 0 SHEET 2 A 7 GLY A 230 CYS A 234 -1 O THR A 233 N MET A 223 SHEET 3 A 7 THR A 274 ILE A 277 -1 O ILE A 277 N GLY A 230 SHEET 4 A 7 MET A 265 VAL A 269 -1 N LYS A 268 O SER A 276 SHEET 5 A 7 ASP A 246 VAL A 253 -1 N ASP A 246 O ILE A 267 SHEET 6 A 7 GLY A 289 GLN A 294 -1 O ILE A 291 N SER A 251 SHEET 7 A 7 SER A 218 THR A 225 -1 N ALA A 219 O VAL A 292 CISPEP 1 ASN A 228 PRO A 229 1 -1.94 CISPEP 2 ASN A 228 PRO A 229 2 -2.12 CISPEP 3 ASN A 228 PRO A 229 3 -2.40 CISPEP 4 ASN A 228 PRO A 229 4 -2.03 CISPEP 5 ASN A 228 PRO A 229 5 -1.73 CISPEP 6 ASN A 228 PRO A 229 6 -4.14 CISPEP 7 ASN A 228 PRO A 229 7 -1.04 CISPEP 8 ASN A 228 PRO A 229 8 -1.64 CISPEP 9 ASN A 228 PRO A 229 9 -0.68 CISPEP 10 ASN A 228 PRO A 229 10 -2.16 CISPEP 11 ASN A 228 PRO A 229 11 -1.99 CISPEP 12 ASN A 228 PRO A 229 12 -1.51 CISPEP 13 ASN A 228 PRO A 229 13 -0.57 CISPEP 14 ASN A 228 PRO A 229 14 -1.19 CISPEP 15 ASN A 228 PRO A 229 15 -0.46 CISPEP 16 ASN A 228 PRO A 229 16 -1.24 CISPEP 17 ASN A 228 PRO A 229 17 -2.27 CISPEP 18 ASN A 228 PRO A 229 18 -1.06 CISPEP 19 ASN A 228 PRO A 229 19 -1.12 CISPEP 20 ASN A 228 PRO A 229 20 -0.65 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