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- SASDDM2: Sinorhizobium meliloti Proline Utilization A (PutA) at 2.00 mg/ml -

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Basic information

Entry
Database: SASBDB / ID: SASDDM2
SampleSinorhizobium meliloti Proline Utilization A (PutA) at 2.00 mg/ml
  • Sinorhizobium meliloti (SmPutA) (protein), SmPutA, Sinorhizobium meliloti
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
Similarity search - Function
Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase ...Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Bifunctional protein PutA
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
CitationJournal: J Biol Chem / Year: 2016
Title: Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function.
Authors: Min Luo / Thameesha T Gamage / Benjamin W Arentson / Katherine N Schlasner / Donald F Becker / John J Tanner /
Abstract: Aldehyde dehydrogenases (ALDHs) catalyze the NAD(P)-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. Although the ALDH superfamily fold is ...Aldehyde dehydrogenases (ALDHs) catalyze the NAD(P)-dependent oxidation of aldehydes to carboxylic acids and are important for metabolism and detoxification. Although the ALDH superfamily fold is well established, some ALDHs contain an uncharacterized domain of unknown function (DUF) near the C terminus of the polypeptide chain. Herein, we report the first structure of a protein containing the ALDH superfamily DUF. Proline utilization A from Sinorhizobium meliloti (SmPutA) is a 1233-residue bifunctional enzyme that contains the DUF in addition to proline dehydrogenase and l-glutamate-γ-semialdehyde dehydrogenase catalytic modules. Structures of SmPutA with a proline analog bound to the proline dehydrogenase site and NAD bound to the ALDH site were determined in two space groups at 1.7-1.9 Å resolution. The DUF consists of a Rossmann dinucleotide-binding fold fused to a three-stranded β-flap. The Rossmann domain resembles the classic ALDH superfamily NAD-binding domain, whereas the flap is strikingly similar to the ALDH superfamily dimerization domain. Paradoxically, neither structural element performs its implied function. Electron density maps show that NAD does not bind to the DUF Rossmann fold, and small-angle X-ray scattering reveals a novel dimer that has never been seen in the ALDH superfamily. The structure suggests that the DUF is an adapter domain that stabilizes the aldehyde substrate binding loop and seals the substrate-channeling tunnel via tertiary structural interactions that mimic the quaternary structural interactions found in non-DUF PutAs. Kinetic data for SmPutA indicate a substrate-channeling mechanism, in agreement with previous studies of other PutAs.
Contact author
  • John Tanner (Mizzou, University of Missouri-Columbia, Columbia, MO, USA)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1718
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.1879015356
Search similar-shape structures of this assembly by Omokage search (details)
Model #1719
Type: mix / Radius of dummy atoms: 1.90 A / Chi-square value: 1.1879015356
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Sinorhizobium meliloti Proline Utilization A (PutA) at 2.00 mg/ml
Specimen concentration: 2 mg/ml
BufferName: 50 mM Tris, 1% (v/v) glycerol, 0.5 mM THP, and 50 mM NaCl
pH: 7.8
Entity #933Name: SmPutA / Type: protein / Description: Sinorhizobium meliloti (SmPutA) / Formula weight: 131.805 / Num. of mol.: 1 / Source: Sinorhizobium meliloti / References: UniProt: F7X6I3
Sequence: SMMSPNPLQK PAIDAAPAPF ADFAPPVRPQ STLRRAITAA YRRPETECLP PLVEAATQSK EIRDAAASTA RKLIEALRGK HSGSGVEGLV QEYSLSSQEG VALMCLAEAL LRIPDTATRD ALIRDKIADG NWKSHLGGSR SLFVNAATWG LVVTGKLTST VNDRSLAAAL ...Sequence:
SMMSPNPLQK PAIDAAPAPF ADFAPPVRPQ STLRRAITAA YRRPETECLP PLVEAATQSK EIRDAAASTA RKLIEALRGK HSGSGVEGLV QEYSLSSQEG VALMCLAEAL LRIPDTATRD ALIRDKIADG NWKSHLGGSR SLFVNAATWG LVVTGKLTST VNDRSLAAAL TRLISRCGEP VIRRGVDMAM RMMGEQFVTG ETIREALKRS KELEEKGFSY SYDMLGEAAT TAADAERYYR DYESAIHAIG KASAGRGIYE GPGISIKLSA LHPRYSRAQA ARVMGELLPR VKALALLAKN YDIGLNIDAE EADRLELSLD LLEVLCLDGD LSGWNGMGFV VQAYGKRCPF VLDFIIDLAR RSGRRIMVRL VKGAYWDAEI KRAQLDGLAD FPVFTRKIHT DVSYIACAAK LLAATDVVFP QFATHNAQTL AAIYHMAGKD FHVGKYEFQC LHGMGEPLYE EVVGRGKLDR PCRIYAPVGT HETLLAYLVR RLLENGANSS FVHRINDPKV SIDELIADPV EVVRAMPVVG AKHDRIALPA ELFGDARTNS AGLDLSNEET LASLTEALRE SAAMKWTALP QLATGPAAGE TRTVLNPGDH RDVVGSVTET SEEDARRAVR LAADAAPDWA AVPPSERAAC LDRAAELMQA RMPTLLGLII REAGKSALNA IAEVREAIDF LRYYAEQTRR TLGPGHGPLG PIVCISPWNF PLAIFTGQIA AALVAGNPVL AKPAEETPLI AAEGVRILRE AGIPASALQL LPGDGRVGAA LVAAAETAGV MFTGSTEVAR LIQAQLADRL SPAGRPIPLI AETGGQNAMI VDSSALAEQV VGDVITSAFD SAGQRCSALR VLCLQEDVAD RILTMLKGAL HELHIGRTDR LSVDVGPVIT SEAKDNIEKH IERMRGLGRK VEQIGLASET GVGTFVPPTI IELEKLSDLQ REVFGPVLHV IRYRRDDLDR LVDDVNATGY GLTFGLHTRL DETIAHVTSR IKAGNLYINR NIIGAVVGVQ PFGGRGLSGT GPKAGGPLYL GRLVTTAPVP PQHSSVHTDP VLLDFAKWLD GKGARAEAEA ARNAGSSSAL GLDLELPGPV GERNLYTLHA RGRILLVPAT ESGLYHQLAA ALATGNSVAI DAASGLQASL KNLPQTVGLR VSWSKDWAAD GPFAGALVEG DAERIRAVNK AIAALPGPLL LVQAASSGEI ARNPDAYCLN WLVEEVSASI NTAAAGGNAS LMAIG

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Experimental information

BeamInstrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS)
City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1127 Å
DetectorName: MAR 165 CCD
Scan
Title: Sinorhizobium meliloti Proline Utilization A (PutA) concentration 2
Measurement date: Mar 27, 2014 / Cell temperature: 10 °C / Unit: 1/A /
MinMax
Q0.0094 0.3256
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 520 /
MinMax
Q0.009426 0.325614
P(R) point1 520
R0 119
Result
Type of curve: single_conc
Comments: The fit to the SAXS data is shown for a volume-fraction weighted mixture of monomers and dimers. The volume fraction of monomer and dimer are 0.73 and 0.27, respectively.
ExperimentalPorod
MW169.77 kDa-
Volume-225 nm3

P(R)GuinierGuinier error
Forward scattering, I0939.7 963.17 10
Radius of gyration, Rg3.8 nm3.838 nm0.05

MinMax
D-11.9
Guinier point1 40

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