5KF6

Structure of proline utilization A from Sinorhizobium meliloti complexed with L-tetrahydrofuroic acid and NAD+ in space group P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of Proline Utilization A (PutA) Reveal the Fold and Functions of the Aldehyde Dehydrogenase Superfamily Domain of Unknown Function.

Luo, M.Gamage, T.T.Arentson, B.W.Schlasner, K.N.Becker, D.F.Tanner, J.J.

(2016) J.Biol.Chem. 291: 24065-24075

  • DOI: 10.1074/jbc.M116.756965
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aldehyde dehydrogenases (ALDHs) catalyze the NAD(P) <sup>+ </sup>-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 ...

    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.


    Organizational Affiliation

    From the Departments of Chemistry and.,From the Departments of Chemistry and tannerjj@missouri.edu.,the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588.,Biochemistry, University of Missouri, Columbia, Missouri 65211, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein PutA
A, B
1235Sinorhizobium meliloti (strain SM11)Mutation(s): 0 
Gene Names: putA
Find proteins for F7X6I3 (Sinorhizobium meliloti (strain SM11))
Go to UniProtKB:  F7X6I3
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TFB
Query on TFB

Download SDF File 
Download CCD File 
A, B
TETRAHYDROFURAN-2-CARBOXYLIC ACID
C5 H8 O3
UJJLJRQIPMGXEZ-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 101.400α = 90.00
b = 102.332β = 106.53
c = 125.909γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-12 
  • Released Date: 2016-10-05 
  • Deposition Author(s): Tanner, J.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM065546
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM061068
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP30GM103335
National Science Foundation (United States)United StatesDBI-1156692

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Type: Database references
  • Version 1.2: 2016-11-23
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence