HEADER ISOMERASE 27-JAN-10 2KTD
TITLE SOLUTION STRUCTURE OF MOUSE LIPOCALIN-TYPE PROSTAGLANDIN D SYNTHASE /
TITLE 2 SUBSTRATE ANALOG (U-46619) COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROSTAGLANDIN-H2 D-ISOMERASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: LIPOCALIN-TYPE PROSTAGLANDIN-D SYNTHASE, GLUTATHIONE-
COMPND 5 INDEPENDENT PGD SYNTHETASE, PROSTAGLANDIN-D2 SYNTHASE, PGD2 SYNTHASE,
COMPND 6 PGDS2, PGDS;
COMPND 7 EC: 5.3.99.2;
COMPND 8 ENGINEERED: YES;
COMPND 9 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 GENE: PTGDS;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-2T
KEYWDS LIPOCALIN-TYPE PROSTAGLANDIN D SYNTHASE, L-PGDS, PROSTAGLANDIN H2,
KEYWDS 2 PROSTAGLANDIN D2, U-46619, LIPOCALIN, DISULFIDE BOND, ENDOPLASMIC
KEYWDS 3 RETICULUM, FATTY ACID BIOSYNTHESIS, GLYCOPROTEIN, GOLGI APPARATUS,
KEYWDS 4 ISOMERASE, LIPID SYNTHESIS, NUCLEUS, PROSTAGLANDIN BIOSYNTHESIS,
KEYWDS 5 PYRROLIDONE CARBOXYLIC ACID, SECRETED, TRANSPORT
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR S.SHIMAMOTO,H.MARUO,T.YOSHIDA,N.KATO,T.OHKUBO
REVDAT 2 01-MAY-24 2KTD 1 REMARK SEQADV
REVDAT 1 02-FEB-11 2KTD 0
JRNL AUTH S.SHIMAMOTO,H.MARUO,T.YOSHIDA,T.INUI,Y.MIYAMOTO,Y.KOBAYASHI,
JRNL AUTH 2 T.TSURUMURA,K.ARITAKE,Y.URADE,T.OHKUBO
JRNL TITL SOLUTION STRUCTURE OF LIPOCALIN-TYPE PROSTAGLANDIN D
JRNL TITL 2 SYNTHASE / SUBSTRATE ANALOG COMPLEX REVEALS OPEN-CLOSED
JRNL TITL 3 CONFORMATIONAL CHANGE REQUIRED FOR SUBSTRATE RECOGNITION
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRVIEW, CNS
REMARK 3 AUTHORS : JOHNSON, ONE MOON SCIENTIFIC (NMRVIEW),
REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,
REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2KTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-10.
REMARK 100 THE DEPOSITION ID IS D_1000101549.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300.5
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 1.0MM [U-15N] PROTEIN; 1.5MM 15
REMARK 210 -HYDROXY-11ALPHA,9ALPHA-(EPOXYMETHANO)PROSTA-5,13-DIENOIC ACID;
REMARK 210 90% H2O/10% D2O; 1.0MM [U-13C; U-15N] PROTEIN; 1.5MM 15-HYDROXY-
REMARK 210 11ALPHA,9ALPHA-(EPOXYMETHANO)PROSTA-5,13-DIENOIC ACID; 90% H2O/
REMARK 210 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D
REMARK 210 CBCA(CO)NH; 3D HCCH-TOCSY; 3D 1H-
REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D
REMARK 210 HBHA(CO)NH
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CNS
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1500
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15
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 ASP A 28 160.62 172.09
REMARK 500 1 ASN A 33 46.14 95.96
REMARK 500 1 ALA A 46 -45.57 -138.75
REMARK 500 1 CYS A 65 -160.71 -174.12
REMARK 500 1 ARG A 85 167.78 56.64
REMARK 500 1 LYS A 86 92.54 82.16
REMARK 500 1 ASN A 87 -62.01 68.45
REMARK 500 1 THR A 91 87.97 -166.86
REMARK 500 1 SER A 108 108.62 -52.29
REMARK 500 1 HIS A 111 35.71 159.15
REMARK 500 1 SER A 112 -71.21 74.78
REMARK 500 1 SER A 114 89.79 38.40
REMARK 500 1 GLU A 122 -86.48 -170.88
REMARK 500 1 ALA A 123 130.43 63.92
REMARK 500 1 ASP A 126 7.66 54.54
REMARK 500 1 PRO A 139 -32.34 -38.65
REMARK 500 1 THR A 152 -29.19 -144.76
REMARK 500 1 GLN A 153 42.48 81.65
REMARK 500 1 LEU A 172 -179.64 -52.27
REMARK 500 1 LEU A 180 59.28 30.97
REMARK 500 1 PRO A 181 156.95 -49.99
REMARK 500 1 GLN A 188 48.22 -104.56
REMARK 500 2 ASP A 28 147.55 -176.96
REMARK 500 2 THR A 29 -79.78 -148.13
REMARK 500 2 ASN A 33 59.51 85.18
REMARK 500 2 ALA A 46 -43.19 -158.84
REMARK 500 2 TYR A 63 -159.50 -98.46
REMARK 500 2 CYS A 65 -163.19 -171.59
REMARK 500 2 LEU A 84 104.58 -170.21
REMARK 500 2 ARG A 85 -37.51 179.88
REMARK 500 2 LYS A 86 -66.02 -90.05
REMARK 500 2 ASN A 87 -35.83 -174.16
REMARK 500 2 THR A 91 114.81 -171.69
REMARK 500 2 ILE A 93 113.84 -167.42
REMARK 500 2 SER A 108 102.32 -59.24
REMARK 500 2 HIS A 111 14.98 104.27
REMARK 500 2 SER A 112 -52.13 78.34
REMARK 500 2 SER A 114 78.14 37.31
REMARK 500 2 GLU A 122 -96.03 -171.63
REMARK 500 2 ALA A 123 136.19 66.74
REMARK 500 2 ASP A 126 7.01 59.97
REMARK 500 2 PRO A 139 -33.64 -36.94
REMARK 500 2 THR A 152 -33.33 -161.45
REMARK 500 2 GLN A 153 46.95 81.94
REMARK 500 2 LEU A 172 178.89 -49.51
REMARK 500 2 LEU A 180 94.12 -35.47
REMARK 500 2 PRO A 183 62.14 -67.24
REMARK 500 2 LYS A 185 -80.64 -43.68
REMARK 500 2 ALA A 186 139.24 62.01
REMARK 500 2 GLN A 188 47.48 -96.33
REMARK 500
REMARK 500 THIS ENTRY HAS 371 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PUC A 200
DBREF 2KTD A 25 189 UNP O09114 PTGDS_MOUSE 25 189
SEQADV 2KTD GLY A 23 UNP O09114 EXPRESSION TAG
SEQADV 2KTD SER A 24 UNP O09114 EXPRESSION TAG
SEQADV 2KTD ALA A 89 UNP O09114 CYS 89 ENGINEERED MUTATION
SEQADV 2KTD ALA A 186 UNP O09114 CYS 186 ENGINEERED MUTATION
SEQRES 1 A 167 GLY SER GLN GLY HIS ASP THR VAL GLN PRO ASN PHE GLN
SEQRES 2 A 167 GLN ASP LYS PHE LEU GLY ARG TRP TYR SER ALA GLY LEU
SEQRES 3 A 167 ALA SER ASN SER SER TRP PHE ARG GLU LYS LYS ALA VAL
SEQRES 4 A 167 LEU TYR MET CYS LYS THR VAL VAL ALA PRO SER THR GLU
SEQRES 5 A 167 GLY GLY LEU ASN LEU THR SER THR PHE LEU ARG LYS ASN
SEQRES 6 A 167 GLN ALA GLU THR LYS ILE MET VAL LEU GLN PRO ALA GLY
SEQRES 7 A 167 ALA PRO GLY HIS TYR THR TYR SER SER PRO HIS SER GLY
SEQRES 8 A 167 SER ILE HIS SER VAL SER VAL VAL GLU ALA ASN TYR ASP
SEQRES 9 A 167 GLU TYR ALA LEU LEU PHE SER ARG GLY THR LYS GLY PRO
SEQRES 10 A 167 GLY GLN ASP PHE ARG MET ALA THR LEU TYR SER ARG THR
SEQRES 11 A 167 GLN THR LEU LYS ASP GLU LEU LYS GLU LYS PHE THR THR
SEQRES 12 A 167 PHE SER LYS ALA GLN GLY LEU THR GLU GLU ASP ILE VAL
SEQRES 13 A 167 PHE LEU PRO GLN PRO ASP LYS ALA ILE GLN GLU
HET PUC A 200 59
HETNAM PUC (5Z)-7-{(1R,4S,5S,6R)-6-[(1E,3S)-3-HYDROXYOCT-1-EN-1-
HETNAM 2 PUC YL]-2-OXABICYCLO[2.2.1]HEPT-5-YL}HEPT-5-ENOIC ACID
HETSYN PUC 15-HYDROXY-11 ALPHA,9 ALPHA-(EPOXYMETHANO)PROSTA-5,13-
HETSYN 2 PUC DIENOIC ACID
FORMUL 2 PUC C21 H34 O4
HELIX 1 1 GLN A 35 PHE A 39 5 5
HELIX 2 2 PHE A 55 ALA A 60 1 6
HELIX 3 3 LYS A 156 GLY A 171 1 16
SHEET 1 A 9 GLY A 41 SER A 50 0
SHEET 2 A 9 LYS A 66 ALA A 70 -1 O VAL A 69 N GLY A 41
SHEET 3 A 9 LEU A 77 PHE A 83 -1 O THR A 80 N VAL A 68
SHEET 4 A 9 GLU A 90 PRO A 98 -1 O GLU A 90 N PHE A 83
SHEET 5 A 9 TYR A 105 TYR A 107 -1 O THR A 106 N GLN A 97
SHEET 6 A 9 SER A 117 SER A 119 -1 O VAL A 118 N TYR A 105
SHEET 7 A 9 ALA A 129 ARG A 134 -1 O PHE A 132 N SER A 119
SHEET 8 A 9 MET A 145 SER A 150 -1 O THR A 147 N LEU A 131
SHEET 9 A 9 GLY A 41 SER A 50 -1 N GLY A 47 O LEU A 148
SITE 1 AC1 11 SER A 45 LEU A 48 LYS A 58 LEU A 62
SITE 2 AC1 11 TYR A 63 CYS A 65 THR A 67 SER A 81
SITE 3 AC1 11 GLU A 90 TYR A 107 PRO A 110
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