Crystal Structure of Fibroblast Growth Factor 9 (FGF9) Reveals Regions. Implicated in Dimerization and Autoinhibition
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1 JBC Papers in Press. Published on November 1, 2000 as Manuscript M Crystal Structure of Fibroblast Growth Factor 9 (FGF9) Reveals Regions Implicated in Dimerization and Autoinhibition 1 Copyright 2000 by The American Society for Biochemistry and Molecular Biology, Inc.
2 β β β 2
3 β β β β 3
4 β β 4
5 β 5
6 µ 6
7 µ µ 7
8 β α β β β β β β β β β β β 8
9 β β α α β α α α µ µ µ 9
10 β β β α α β 10
11 β β β β β β β β β through interactions between the FGF N-terminal (immediately preceding the β-trefoil core) 11
12 and central regions with two loop regions in FGFR D3 that are subject to alternative splicing (32). β β β α β β β β β 12
13 β 13
14 β β 14
15 β 15
16 16
17 17
18 30. Moniatte, M., Lesieur, C., Vecsey-Semjen, B., Buckley, J. T., Pattus, F., van der Goot, F. G., and Van Dorsselaer, A 31. Jespersen, S., Niessen, W. M., Tjaden, U. R., and van der Greef, J. (1998)
19 Table 1. Summary of Crystallographic Analysis Data Collection Statistics Resolution (Å) Reflections (total/unique) Completeness (%) a R sym (%) Signal ( I / σi ) / (100) b 8.1 (26.4) b 10.4 Refinement Statistics c Root-mean-square Deviations Resolution (Å) Reflections d R cryst / R free (%) Bonds (Å) Angles ( ) B-factors e (Å 2 ) / a Rsym = 100 x Σ hkl Σ i I i (hkl) I(hkl) / Σ hkl Σ i I i (hkl). b Value in parentheses is for the highest resolution shell: Å. c Atomic model: 1246 protein atoms, 2 PO4 ions and 68 water molecules. d Rcryst/free = 100 x Σ hkl F o (hkl) F c (hkl) / Σ hkl F o (hkl), where F o (>2σ) and F c are the observed and calculated structure factors, respectively. 5% of the reflections were used for calculation of R free. e For bonded protein atoms. 19
20 Figure Legends Figure 1. Ribbon diagram of FGF9. Secondary structure assignments were obtained with the program PROCHECK (37). The β strands of FGF9 are labeled according to the conventional strand nomenclature for FGF1 and FGF2 (38). NT and CT denote the amino- and carboxy-termini. This figure was created using the programs Molscript (39) and Raster3D (40). Figure 2. FGF9 dimerizes in solution. A, 1 ml of purified FGF9 solutions of decreasing concentrations [black 2mg/ml, blue 0.5mg/ml, green 40 µg/ml, brown 20 µg/ml, red 8 µg/ml] were analyzed by size exclusion chromatography. Arrows indicate the position of the size standards [67 kda, Albumin; 43 kda, Ovalbumin; 25 kda, Chymotrypsinogen; 13.7 kda, Ribonuclease A]. B, Sedimentation equilibrium analysis of FGF9 was performed with sample concentrations ranging from 1.6 µm to 26 µm. Distribution of FGF9 in the cell was determined by absorbance at 278 nm (at 12000, and 24,000 rpm) or 235 nm (at 18000, and rpm). A total of 18 different datasets could be fit globally only to a simple dimerization model in which FGF9 dimerizes with a K D of 680 nm (see text). Data for four different concentrations are shown (1.6 µm, 3.3 µm, 6.6 µm, and 13.2 µm), each at three different speeds. Symbols correspond to datapoints, and the curve through the symbols corresponds to the global best fit. Residuals for this fit are plotted in the upper panel for each dataset, and are both small and randomly distributed. Residual plots have been arbitrarily displaced along the y-axis for clarity. C, MALDI-MS analysis of 1pmol of FGF-9 using sinapinic acid as the matrix in 30% acetonitrile. Detected in the mass spectrum are clear signals for the monomeric FGF9 at m/z 20,169 and dimeric FGF9 at m/z 40,230. No higher order oligomers are observed. 20
21 Figure. 3. The two-fold crystallographic FGF9 dimer. A, ribbon diagram of the FGF9 dimer. The two FGF9 protomers are colored orange and red, respectively. B, space-filling model of the FGF9 dimer (same orientation as in Part A). Coloring of the protomers is the same as in Part A. FGF9 residues that participate in dimer formation are colored only in one of the protomers. FGF9 residues are considered to be in the dimer interface only if one pair of atoms (side chain or main chain) has an inter-atomic distance of less than or equal to 3.8 Å. In addition, dimer interface residues that are predicted to be in the receptor interface are colored with respect to the FGFR region with which they would interact. FGF9 residues that are predicted to interact with D2 are colored green, residues that are predicted to interact with the linker region are colored gray, and residues that are predicted to interact with D3 are colored cyan. C, space-filling representation of the dimer interface. The dimer, shown in part B, was rotated 90 about the vertical axis as indicated and one of the protomers (red) was removed to improve visualization of the dimer interface. Interface residues that are predicted to participate in FGFR binding are labeled. This figure was created using Molscript and Raster3D. Figure 4. Detailed interactions at the FGF9 dimer interface. A, stereo view of the portion of the dimer interface outside the β-trefoil core. B, stereo view of the portion of the dimer interface inside the β-trefoil core. The coloring of the protomers is the same as in Figure 3. Oxygen atoms are colored red, nitrogen atoms are blue and carbon atoms have the same coloring as the protomers to which they belong. Only side chains of interacting residues are shown. Dotted lines represent hydrogen bonds. At the right side of each stereo pair, a view of the whole structure in the exact orientation as in stereo view is shown and the region of interest is highlighted. This figure was created using Molscript and Raster3D. 21
22 Figure 5. Structure-based sequence alignment of FGFs. Sequence alignment was performed using the CLUSTALW (41). All of the FGFs used in this alignment are human. β α α β α β β This figure was created using Molscript and Raster3D. α α 22
23 Dotted lines represent hydrogen bonds. This figure was created using Molscript and Raster3D. 23
24 CT αc β2 β1 β3 β11 β12 NT αn β6 β7 β5 β4 Figure 1 β10 β8 β9
25 A Figure 2 Absorbance at 280 nm B Residuals 0.01 per div Elution Volume (ml) µg/ml 20 µg/ml 40 µg/ml 0.5 mg/ml 2 mg/ml OD OD 0.1 OD Radius (cm) Radius (cm) Radius (cm) C monomer 20,169 dimer 40,230 m/z
26 A C Y67 H73 L188 W144 R190 P189 B 90 I60 L61 Figure 3
27 Figure 4 A R62 B I204 L54 L54 I204 K58 L200 I60 L61 D193 K58 R62 D195 L200 I60 L61 D195 D193 R64 R64 N143 N143 Y67 Y67 Y145 Y145 L188 W144 L188 W144 R190 R190
28 FGF9 MAPLGEVGNYFGVQDAVPFGNVPVLPVDSPVLLSDHLGQSEAGGLPRGPAVT FGF16 MAEVGGVFASLDW.LHG.SSSLGNVPLADSPGFLNERLGQIE.KLQRGSP. FGF1 MAE.EITTFTALTEKFN- FGF2 MAA.SITTLPALPEDGGS FGF4 MSGPGTAAVALLPAVLLALLAPWA.RG.AAAPTAPNGTLEAELERRWE.L.A..LARLPVA.QPKEAAVQSG FGF7 MHKWILTWILPTLLYRSCFHIICL.GTISLACNDMTPEQMATNVNCSS.ERHTRS FGF10 MWKWILTHCASAFPHLPGCCCCCFLLLFLVSS..VTCQALGQDMVSPEATNSSSS.FSSPSSA.RH.R hhhhhhhhn bbbbb1 bbbbb2 bbbb3 bbbbbbb4 bbbbbb5 bbbbb6 bbbb7 FGF9 53 DLDHLKGILRRRQLYCRTG--FHLEIFPNGTIQGTRKDHSRFGILEFISIAVGLVSIRGVDSGLYLGMNEKGELYGSEK FGF16 52.FA VH...H...I...R...K. FGF LPPGNYKKPKL...SN.-GHF.R.L.D..VD...DRSDQHIQ.QLSAES..E.Y.KSTET.Q..A.DTD.L...QT FGF2 19 GAFPPGHFKDPKR...KN.-G.F.R.H.D.RVD.V.EKSDPHIK.QLQAEER.V...K..CANR..A.K.D.R.LA.KC FGF4 73 AG.Y.L..K.L.R...NV.IG...QAL.D.R.G.AHA.T-.DSL..LSPVER.V...F..A.RFFVA.SS..K...PF FGF7 56 YDYMEG.DI.V.R.F...Q--WY.R.DKR.KVK..QEMKNNYN.M.IRTV...I.A.K..E.EF..A..KE.K..AKKE FGF10 69 SYNHLQ.DV.W.K.FSF.K--YF.K.EK..KVS..K.ENCPYS...IT.VEI.V.AVKAIN.NY..A..K..K...KE bbbbb8 bbbbb9 bbb10 bbb11 bbbbb12 hhhhc FGF9 130 LTQECVFREQFEENWYNTYSSNLYKHVDTGRRYYVALNKDGTPREGTRTKRHQKFTHFLPRPVDPDKVPELYKDILSQS FGF R...A.T...S.SE.Q...S...Y...S.L.SMSR.LFHYR FGF1 94 PNE..L.L.RL...H...I.KKHAEKN----WF.G.K.N.SCK..P..HYG..AIL...L..SS. FGF2 97 V.D..F.F.RL.S.N...R.RK.TS------W...KRT.QYKL.SK.GPG..AIL...MSAKS FGF4 151 F.D..T.K.ILLP.N..A.E.YK.PG------MFI..S.N.KTKK.N.VSPTM.V...L FGF7 133 CNED.N.K.LIL..H...A.AKWT.NGGE--MF...QK.I.VR.KK..KE..TA...MAIT FGF FNND.KLK.RI...G...A.FNWQ.NG--.QM...GK.A..R.QK...KNTSA...MV.HS Figure 5 Downloaded from by guest on August 31, 2018
29 A B H73 R86 H73 R86 Y115 I60 L130 L61 I98 V135 R190 P189 N146 L188 G71 Y67 Y145 Y115 I60 L130 L61 I98 V135 R190 L188 P189 N146 G71 Y67 Y145 I100 A101 V105 E138 S99 G103 W144 Y140 I100 A101 V105 E138 S99 G103 W144 Y140 V102 V102 Figure 6
30 A B K121 E123 T158 K154 R137 R161 T176 Y163 R160 R180 K179 H181 E174 R177 Q182 K183 R173 N167 T70 T171 K168 R69 K121 E123 T158 K154 R137 R161 T176 Y163 R160 R180 K179 H181 E174 R177 Q182 K183 R173 N167 T70 T171 K168 R69 T81 D169 T81 D169 Figure 7
31 Crystal structure of fibroblast growth factor 9 (FGF9) reveals regions implicated in dimerization and autoinhibition Alexander N. Plotnikov, Anna V. Eliseenkova, Omar A. Ibrahimi, Zachary Shriver, Ram Sasisekharan, Mark A. Lemmon and Moosa Mohammadi J. Biol. Chem. published online November 1, 2000 Access the most updated version of this article at doi: /jbc.M Alerts: When this article is cited When a correction for this article is posted Click here to choose from all of JBC's alerts
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