3PEF

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter metallireducens in complex with NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural characterization of a beta-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity.

Zhang, Y.Zheng, Y.Qin, L.Wang, S.Buchko, G.W.Garavito, R.M.

(2014) Biochimie 104: 61-69

  • DOI: 10.1016/j.biochi.2014.05.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beta-hydroxyacid dehydrogenase (β-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD(+)- or NADP(+)-dependent oxidation of various β-hydroxy acid substrates into their correspo ...

    Beta-hydroxyacid dehydrogenase (β-HAD) genes have been identified in all sequenced genomes of eukaryotes and prokaryotes. Their gene products catalyze the NAD(+)- or NADP(+)-dependent oxidation of various β-hydroxy acid substrates into their corresponding semialdehyde. In many fungal and bacterial genomes, multiple β-HAD genes are observed leading to the hypothesis that these gene products may have unique, uncharacterized metabolic roles specific to their species. The genomes of Geobacter sulfurreducens and Geobacter metallireducens each contain two potential β-HAD genes. The protein sequences of one pair of these genes, Gs-βHAD (Q74DE4) and Gm-βHAD (Q39R98), have 65% sequence identity and 77% sequence similarity with each other. Both proteins are observed to reduce succinic semialdehyde, a 4-carbon substrate instead of the typical β-HAD 3-carbon substrate, to γ-hydroxybutyric acid. To further explore the structural and functional characteristics of these two β-HADs with a less frequently observed substrate specificity, crystal structures for Gs-βHAD and Gm-βHAD in complex with NADP(+) were determined to a resolution of 1.89 Å and 2.07 Å, respectively. The structures of both proteins are similar, composed of 14 α-helices and nine β-strands organized into two domains. Domain 1 (1-165) adopts a typical Rossmann fold composed of two α/β units: a six-strand parallel β-sheet surrounded by six α-helices (α1-α6) followed by a mixed three-strand β-sheet surrounded by two α-helices (α7 and α8). Domain 2 (166-287) is composed of a bundle of seven α-helices (α9-α14). Four functional regions conserved in all β-HADs are spatially located near each other, with a buried molecule of NADP(+), at the interdomain cleft. Comparison of these Geobacter structures to a closely related β-HAD from Arabidopsis thaliana in the apo-NADP(+) and apo-substrate bound state suggests that NADP(+) binding effects a rigid body rotation between Domains 1 and 2. Bound near the Substrate-Binding and Catalysis Regions in two of the eight protomers in the asymmetric unit of Gm-βHAD is a glycerol molecule that may mimic features of bound biological substrates.


    Organizational Affiliation

    College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China. Electronic address: wshyyl@sina.com.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824-1319, USA. Electronic address: garavito@msu.edu.,Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Electronic address: garry.buchko@pnnl.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphogluconate dehydrogenase, NAD-binding
A, B, C, D, E, F, G, H
287Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210)Mutation(s): 2 
Gene Names: ghr
Find proteins for Q39R98 (Geobacter metallireducens (strain GS-15 / ATCC 53774 / DSM 7210))
Go to UniProtKB:  Q39R98
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A, B, C, D, E, F, G, H
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, D, E, G, H
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 75.968α = 82.15
b = 79.141β = 88.80
c = 95.470γ = 87.66
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references