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Yorodumi- SASDDP3: N-propargyl glycine-Inactivated Proline utilization A from Bradyr... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDDP3 |
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Sample | N-propargyl glycine-Inactivated Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS
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Function / homology | Function and homology information proline dehydrogenase / proline dehydrogenase activity / 1-pyrroline-5-carboxylate dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / proline catabolic process to glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding / identical protein binding Similarity search - Function |
Biological species | Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria) |
Citation | Journal: Biophys J / Year: 2018 Title: Redox Modulation of Oligomeric State in Proline Utilization A. Authors: David A Korasick / Ashley C Campbell / Shelbi L Christgen / Srinivas Chakravarthy / Tommi A White / Donald F Becker / John J Tanner / Abstract: Homooligomerization of proline utilization A (PutA) bifunctional flavoenzymes is intimately tied to catalytic function and substrate channeling. PutA from Bradyrhizobium japonicum (BjPutA) is unique ...Homooligomerization of proline utilization A (PutA) bifunctional flavoenzymes is intimately tied to catalytic function and substrate channeling. PutA from Bradyrhizobium japonicum (BjPutA) is unique among PutAs in that it forms a tetramer in solution. Curiously, a dimeric BjPutA hot spot mutant was previously shown to display wild-type catalytic activity despite lacking the tetrameric structure. These observations raised the question of what is the active oligomeric state of BjPutA. Herein, we investigate the factors that contribute to tetramerization of BjPutA in vitro. Negative-stain electron microscopy indicates that BjPutA is primarily dimeric at nanomolar concentrations, suggesting concentration-dependent tetramerization. Further, sedimentation-velocity analysis of BjPutA at high (micromolar) concentration reveals that although the binding of active-site ligands does not alter oligomeric state, reduction of the flavin adenine dinucleotide cofactor results in dimeric protein. Size-exclusion chromatography coupled with multiangle light scattering and small-angle x-ray scattering analysis also reveals that reduced BjPutA is dimeric. Taken together, these results suggest that the BjPutA oligomeric state is dependent upon both enzyme concentration and the redox state of the flavin cofactor. This is the first report, to our knowledge, of redox-linked oligomerization in the PutA family. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDDP3 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
Model #1805 | Type: atomic / Chi-square value: 2.9816132533 Search similar-shape structures of this assembly by Omokage search (details) |
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Model #1795 | Type: atomic / Chi-square value: 1.64908802698 Search similar-shape structures of this assembly by Omokage search (details) |
Model #1796 | Type: atomic / Chi-square value: 1.64908802698 Search similar-shape structures of this assembly by Omokage search (details) |
-Sample
Sample | Name: N-propargyl glycine-Inactivated Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS |
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Buffer | Name: 50 mM Tris, 50 mM NaCl, 0.5 mM TCEP, 5% (v/v) glycerol pH: 7.8 |
Entity #976 | Name: BjPutA / Type: protein / Description: Bifunctional protein PutA / Formula weight: 107.558 / Num. of mol.: 2 Source: Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) References: UniProt: Q89E26 Sequence: GHMPNIPPPF TAPYAPDDAE IAARLLPASH LSPPQEARIH RTATRLIEAI RKRDDRLGGV EDMLREFALS TKEGLALMVL AEALLRVPDA RTADQFIEDK LGEGDFIHHE TKSTAFLVNA SAWALGLSAR VIQPGETPDG TIGRLVKRLG APAVRTATRQ AMRLMGNHFV ...Sequence: GHMPNIPPPF TAPYAPDDAE IAARLLPASH LSPPQEARIH RTATRLIEAI RKRDDRLGGV EDMLREFALS TKEGLALMVL AEALLRVPDA RTADQFIEDK LGEGDFIHHE TKSTAFLVNA SAWALGLSAR VIQPGETPDG TIGRLVKRLG APAVRTATRQ AMRLMGNHFV LGETIEQALE RGKPRSGQKT RYSFDMLGEG ARTAADARRY FDAYASAIET IGKAAGNHAL PDRPGISVKL SALHPRFEAI SRARVMVELV PQLLDLAQRA KAHDLNFTVD AEEADRLELS LDVIAATLAD PSLKGWDGFG LAIQAYQKRA SAVIDYVDAL ARAHDRKLMV RLVKGAYWDT EIKRAQERGL DGYPVFTRKA MTDLNYVACA SKLLALRPRI FPQFATHNAL TVATVLEMAE GSSGFEFQRL HGMGEALYEQ LAKDHADIAY RTYAPVGSHR DLLAYLVRRL LENGANSSFV AQAADYRVPV PALLQRPADA IVRPQAAAHP RIPLPCDLFA PERRNSRGVE FGARTALDQL LTDVKAETGD LKPIADATPD QAHAAVAAAR AGFAGWSRTP AGIRAAALEQ AAHLLESRSA HFIALLQREG GKTLDDALSE LREAADFCRY YAAQGRKLFG SETAMPGPTG ESNALTMRGR GVFVAISPWN FPLAIFLGQV TAALMAGNSV VAKPAEQTPR IAREAVALLH EAGIPKSALY LVTGDGRIGA ALTAHPDIAG VVFTGSTEVA RSINRALAAK DGPIVPLIAE TGGINAMIAD ATALPEQVAD DVVTSAFRSA GQRCSALRLL FVQEDVADRM IEMVAGAARE LKIGDPSDVA THVGPVIDVE AKQRLDAHIA RMKTEARLHF AGPAPEGCFV APHIFELTEA GQLTEEVFGP ILHVVRYRPE NLERVLRAIE RTGYGLTLGV HSRIDDSIEA IIDRVQVGNI YVNRNMIGAV VGVQPFGGNG LSGTGPKAGG PHYLARFATE QTVTINTAAA GGNAALLAGE E |
-Experimental information
Beam | Instrument name: Advanced Photon Source (APS) BioCAT 18ID / City: Argonne, IL / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.103 Å / Dist. spec. to detc.: 3.5 mm | ||||||||||||||||||||||||||||||
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Detector | Name: Pilatus 100K / Pixsize x: 172 mm | ||||||||||||||||||||||||||||||
Scan | Title: N-propargyl glycine-Inactivated Proline utilization A from Bradyrhizobium diazoefficiens (formerly Bradyrhizobium japonicum) collected by SEC-SAXS Measurement date: Jul 16, 2017 / Cell temperature: 22 °C / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 1264 /
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Result | Type of curve: sec /
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