Bioisis

"Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum"

Experimental SAS Curve

Your browser doesn't support canvas.

Low_res_thumbnail

Experimental Mass

448,000 Da

Experimental Details for BID:  BJPUTP
Experiment ID: 75
Collected at: SIBYLS beamline 12.3.1
Contributors: Hura, GL ,  Tanner, JJ ,  Srivastava, D
The bifunctional proline catabolic flavoenzyme, proline utilization A (PutA), catalyzes the oxidation of proline to glutamate via the sequential activities of FAD-dependent proline dehydrogenase (PRODH) and NAD+-dependent ?1-pyrroline-5-carboxylate dehydrogenase (P5CDH) domains. Although structures for some of the domains of PutA are known, a structure for the full-length protein has not previously been solved. We report the 2.1 Å resolution crystal structure of PutA from Bradyrhizobium japonicum, along with data from small-angle x-ray scattering, analytical ultracentrifugation, and steady-state and rapid-reaction kinetics. PutA forms a ring-shaped tetramer in solution having a diameter of 150 Å. Within each protomer, the PRODH and P5CDH active sites face each other at a distance of 41 Å and are connected by a large, irregularly shaped cavity.
Extrapolated to zero concentration from 4 different concentrations between 1 and 10 mg/mL

Electron Pair Distribution

Your browser doesn't support canvas.

       Dmax → 140 Å


Guinier Plot

Your browser doesn't support canvas.

     Guinier Rg → 52.6 Å

Real Space Rg → 51.9 Å

The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.


Kratky Plot

Your browser doesn't support canvas.

The Kratky plot can be used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape.


GASBOR Model

GASBOR result was determined with the following:

Space GroupP1
Chi2.1
NSD | RMSD1.1 
variance(NSD | RMSD)1.1 
Number of Models in Average10 
Superimposed model10 

Additional Experimental Details
Title

Crystal structure of the bifunctional proline utilization A flavoenzyme from Bradyrhizobium japonicum

Description

The bifunctional proline catabolic flavoenzyme, proline utilization A (PutA), catalyzes the oxidation of proline to glutamate via the sequential activities of FAD-dependent proline dehydrogenase (PRODH) and NAD+-dependent ?1-pyrroline-5-carboxylate dehydrogenase (P5CDH) domains. Although structures for some of the domains of PutA are known, a structure for the full-length protein has not previously been solved. We report the 2.1 Å resolution crystal structure of PutA from Bradyrhizobium japonicum, along with data from small-angle x-ray scattering, analytical ultracentrifugation, and steady-state and rapid-reaction kinetics. PutA forms a ring-shaped tetramer in solution having a diameter of 150 Å. Within each protomer, the PRODH and P5CDH active sites face each other at a distance of 41 Å and are connected by a large, irregularly shaped cavity.

Publication

PNAS Volume: 107 Issue: 7 Pages: 2878-2883 Published: FEB 16 2010

Contributors

Hura, GL ,  Tanner, JJ ,  Srivastava, D

Genomics and Proteomics

The experiment is composed of a single gene/ORF

Abbreviated name: PUTA

Annotation: The. bifunctional. proline. catabolic. flavoenzyme,. proline. utilization. A. (PutA),. catalyzes. the. oxidation. of. proline. to. glutamate. via. the. sequential. activities. of. FAD-dependent. proline. dehydrogenase. (PRODH). and. NAD(+)-dependent. Delta(1)-pyrroline-5-carboxylate. dehydrogenase. (P5CDH). domains.

MPNIPPPFTA PYAPDDAEIA ARLLPASHLS PPQEARIHRT ATRLIEAIRK RDDRLGGVED MLREFALSTK EGLALMVLAE ALLRVPDART ADQFIEDKLG EGDFIHHETK STAFLVNASA WALGLSARVI QPGETPDGTI GRLVKRLGAP AVRTATRQAM RLMGNHFVLG ETIEQALERG KPRSGQKTRY SFDMLGEGAR TAADARRYFD AYASAIETIG KAAGNHALPD RPGISVKLSA LHPRFEAISR ARVMVELVPQ LLDLAQRAKA HDLNFTVDAE EADRLELSLD VIAATLADPS LKGWDGFGLA IQAYQKRASA VIDYVDALAR AHDRKLMVRL VKGAYWDTEI KRAQERGLDG YPVFTRKAMT DLNYVACASK LLALRPRIFP QFATHNALTV ATVLEMAEGS SGFEFQRLHG MGEALYEQLA KDHADIAYRT YAPVGSHRDL LAYLVRRLLE NGANSSFVAQ AADYRVPVPA LLQRPADAIV RPQAAAHPRI PLPCDLFAPE RRNSRGVEFG ARTALDQLLT DVKAETGDLK PIADATPDQA HAAVAAARAG FAGWSRTPAG IRAAALEQAA HLLESRSAHF IALLQREGGK TLDDALSELR EAADFCRYYA AQGRKLFGSE TAMPGPTGES NALTMRGRGV FVAISPWNFP LAIFLGQVTA ALMAGNSVVA KPAEQTPRIA REAVALLHEA GIPKSALYLV TGDGRIGAAL TAHPDIAGVV FTGSTEVARS INRALAAKDG PIVPLIAETG GINAMIADAT ALPEQVADDV VTSAFRSAGQ RCSALRLLFV QEDVADRMIE MVAGAARELK IGDPSDVATH VGPVIDVEAK QRLDAHIARM KTEARLHFAG PAPEGCFVAP HIFELTEAGQ LTEEVFGPIL HVVRYRPENL ERVLRAIERT GYGLTLGVHS RIDDSIEAII DRVQVGNIYV NRNMIGAVVG VQPFGGNGLS GTGPKAGGPH YLARFATEQT VTINTAAAGG NAALLAGEE
categoryamino acid composition(%)
HydrophobicI(5.0) V(6.5) L(10.0) M(1.9) A(16.2) G(8.0) P(5.5)
AromaticF(3.5) W(0.5) Y(2.1)
HydrophilicR(8.2) K(2.9) E(6.2) D(5.6) Q(3.2) N(2.2) H(2.6) S(4.0) T(5.3) C(0.5)