HEADER HYDROLASE 03-MAY-06 2DOS
TITLE STRUCTURAL BASIS FOR THE RECOGNITION OF LYS48-LINKED POLYUBIQUITIN
TITLE 2 CHAIN BY THE JOSEPHIN DOMAIN OF ATAXIN-3, A PUTATIVE DEUBIQUITINATING
TITLE 3 ENZYME
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ATAXIN-3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: JOSEPHIN DOMAIN;
COMPND 5 SYNONYM: MACHADO-JOSEPH DISEASE PROTEIN 1, SPINOCEREBELLAR ATAXIA
COMPND 6 TYPE 3 PROTEIN;
COMPND 7 EC: 3.4.22.-;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1
KEYWDS DEUBIQUITINATING ENZYME, HYDROLASE
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.SUMIYOSHI
REVDAT 4 31-DEC-14 2DOS 1 JRNL
REVDAT 3 03-DEC-14 2DOS 1 JRNL VERSN
REVDAT 2 24-FEB-09 2DOS 1 VERSN
REVDAT 1 22-MAY-07 2DOS 0
JRNL AUTH T.SATOH,A.SUMIYOSHI,M.YAGI-UTSUMI,E.SAKATA,H.SASAKAWA,
JRNL AUTH 2 E.KURIMOTO,Y.YAMAGUCHI,W.LI,C.A.JOAZEIRO,T.HIROKAWA,K.KATO
JRNL TITL MODE OF SUBSTRATE RECOGNITION BY THE JOSEPHIN DOMAIN OF
JRNL TITL 2 ATAXIN-3, WHICH HAS AN ENDO-TYPE DEUBIQUITINASE ACTIVITY.
JRNL REF FEBS LETT. V. 588 4422 2014
JRNL REFN ISSN 0014-5793
JRNL PMID 25448680
JRNL DOI 10.1016/J.FEBSLET.2014.10.013
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.1
REMARK 3 AUTHORS : GUNTERT
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2DOS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-06.
REMARK 100 THE RCSB ID CODE IS RCSB025665.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 10MM SODIUM PHOSPHATE BUFFER
REMARK 210 PRESSURE : 1ATM
REMARK 210 SAMPLE CONTENTS : 1.2MM JOSEPHIN DOMAIN U-15N,13C;
REMARK 210 10MM SODIUM PHOSPHATE BUFFER; 90%
REMARK 210 H2O, 10% D2O; 1.2MM JOSEPHIN
REMARK 210 DOMAIN U-15N,13C; 10MM SODIUM
REMARK 210 PHOSPHATE BUFFER; 99% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N-
REMARK 210 SEPARATED_NOESY; 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 920 MHZ; 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : ECA; AVANCE; DMX
REMARK 210 SPECTROMETER MANUFACTURER : JEOL; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE 2.3, CYANA
REMARK 210 2.1, DELTA 4.3.3
REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED
REMARK 210 ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 MODELS 1-10
REMARK 465 RES C SSSEQI
REMARK 465 GLY A -4
REMARK 465 PRO A -3
REMARK 465 LEU A -2
REMARK 465 GLY A -1
REMARK 465 SER A 0
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 GLU A 7 147.29 -171.61
REMARK 500 1 LEU A 13 102.37 59.39
REMARK 500 1 THR A 54 159.20 179.43
REMARK 500 1 GLN A 64 73.81 63.57
REMARK 500 1 PRO A 65 -177.00 -69.77
REMARK 500 1 SER A 66 -169.72 51.98
REMARK 500 1 ASN A 68 -48.69 -156.96
REMARK 500 1 ASP A 70 -169.71 -111.41
REMARK 500 1 ASP A 71 -68.52 72.64
REMARK 500 1 PHE A 75 -169.09 -79.97
REMARK 500 1 LYS A 117 106.56 -40.63
REMARK 500 1 HIS A 119 145.19 179.39
REMARK 500 2 SER A 3 25.65 -150.83
REMARK 500 2 LYS A 8 101.07 60.28
REMARK 500 2 SER A 55 -75.67 -179.75
REMARK 500 2 GLN A 64 155.33 179.81
REMARK 500 2 PRO A 65 -170.52 -69.72
REMARK 500 2 ASN A 68 34.46 -179.96
REMARK 500 2 MET A 69 -75.54 69.13
REMARK 500 2 ASP A 70 -177.99 57.67
REMARK 500 2 ASP A 71 24.82 -140.91
REMARK 500 2 SER A 72 -75.19 -88.43
REMARK 500 2 PHE A 74 88.02 51.03
REMARK 500 2 SER A 76 171.61 178.18
REMARK 500 2 ARG A 110 -63.43 -108.90
REMARK 500 2 LYS A 117 -87.49 58.77
REMARK 500 3 GLN A 64 153.80 64.32
REMARK 500 3 SER A 66 -68.94 72.27
REMARK 500 3 ASP A 70 -42.45 -179.09
REMARK 500 3 PHE A 75 -174.09 52.97
REMARK 500 3 LYS A 117 106.24 -40.03
REMARK 500 3 HIS A 119 144.10 -179.90
REMARK 500 3 GLU A 158 -71.88 -87.32
REMARK 500 4 SER A 3 28.51 -161.12
REMARK 500 4 GLU A 7 141.25 -179.26
REMARK 500 4 SER A 12 145.05 66.06
REMARK 500 4 GLN A 64 156.95 179.25
REMARK 500 4 PRO A 65 -170.98 -69.74
REMARK 500 4 MET A 69 -169.85 -70.30
REMARK 500 4 ASP A 70 -75.53 -78.06
REMARK 500 4 PHE A 75 -168.94 -61.03
REMARK 500 4 SER A 76 177.07 178.35
REMARK 500 4 LYS A 117 106.69 -43.17
REMARK 500 4 GLU A 118 44.72 70.39
REMARK 500 4 HIS A 119 148.89 179.63
REMARK 500 5 GLU A 2 -61.20 73.70
REMARK 500 5 LYS A 8 109.91 64.08
REMARK 500 5 SER A 12 -74.88 -108.76
REMARK 500 5 THR A 54 163.11 64.38
REMARK 500 5 GLN A 64 69.94 60.53
REMARK 500
REMARK 500 THIS ENTRY HAS 120 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2DOS A 1 171 UNP P54252 ATX3_HUMAN 1 171
SEQADV 2DOS GLY A -4 UNP P54252 CLONING ARTIFACT
SEQADV 2DOS PRO A -3 UNP P54252 CLONING ARTIFACT
SEQADV 2DOS LEU A -2 UNP P54252 CLONING ARTIFACT
SEQADV 2DOS GLY A -1 UNP P54252 CLONING ARTIFACT
SEQADV 2DOS SER A 0 UNP P54252 CLONING ARTIFACT
SEQRES 1 A 176 GLY PRO LEU GLY SER MET GLU SER ILE PHE HIS GLU LYS
SEQRES 2 A 176 GLN GLU GLY SER LEU CYS ALA GLN HIS CYS LEU ASN ASN
SEQRES 3 A 176 LEU LEU GLN GLY GLU TYR PHE SER PRO VAL GLU LEU SER
SEQRES 4 A 176 SER ILE ALA HIS GLN LEU ASP GLU GLU GLU ARG MET ARG
SEQRES 5 A 176 MET ALA GLU GLY GLY VAL THR SER GLU ASP TYR ARG THR
SEQRES 6 A 176 PHE LEU GLN GLN PRO SER GLY ASN MET ASP ASP SER GLY
SEQRES 7 A 176 PHE PHE SER ILE GLN VAL ILE SER ASN ALA LEU LYS VAL
SEQRES 8 A 176 TRP GLY LEU GLU LEU ILE LEU PHE ASN SER PRO GLU TYR
SEQRES 9 A 176 GLN ARG LEU ARG ILE ASP PRO ILE ASN GLU ARG SER PHE
SEQRES 10 A 176 ILE CYS ASN TYR LYS GLU HIS TRP PHE THR VAL ARG LYS
SEQRES 11 A 176 LEU GLY LYS GLN TRP PHE ASN LEU ASN SER LEU LEU THR
SEQRES 12 A 176 GLY PRO GLU LEU ILE SER ASP THR TYR LEU ALA LEU PHE
SEQRES 13 A 176 LEU ALA GLN LEU GLN GLN GLU GLY TYR SER ILE PHE VAL
SEQRES 14 A 176 VAL LYS GLY ASP LEU PRO ASP
HELIX 1 1 CYS A 14 LEU A 23 1 10
HELIX 2 2 SER A 29 GLU A 50 1 22
HELIX 3 3 THR A 54 GLN A 63 1 10
HELIX 4 4 SER A 76 VAL A 86 1 11
HELIX 5 5 SER A 96 ARG A 103 1 8
HELIX 6 6 SER A 144 GLY A 159 1 16
SHEET 1 A 6 GLU A 90 LEU A 93 0
SHEET 2 A 6 SER A 161 LYS A 166 -1 O LYS A 166 N GLU A 90
SHEET 3 A 6 SER A 111 TYR A 116 -1 N ILE A 113 O PHE A 163
SHEET 4 A 6 HIS A 119 LEU A 126 -1 O VAL A 123 N PHE A 112
SHEET 5 A 6 GLN A 129 LEU A 133 -1 O PHE A 131 N ARG A 124
SHEET 6 A 6 GLU A 141 ILE A 143 -1 O ILE A 143 N TRP A 130
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
(ATOM LINES ARE NOT SHOWN.)
END
