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

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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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: https://doi.org/10.1016/j.biochi.2014.05.002
  • Primary Citation of Related Structures:  
    3PDU, 3PEF

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase, NAD-binding
A, B, C, D, E
A, B, C, D, E, F, G, H
287Geobacter metallireducensMutation(s): 2 
Gene Names: Gmet_3011
Find proteins for Q39R98 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39R98 
Go to UniProtKB:  Q39R98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39R98
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
BA [auth H]
I [auth A]
O [auth B]
Q [auth C]
S [auth D]
BA [auth H],
I [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
Y [auth F],
Z [auth G]
C21 H28 N7 O17 P3
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth G],
CA [auth H],
M [auth A],
T [auth D],
X [auth E]
C4 H10 O3
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
P [auth B]
R [auth C]
J [auth A],
K [auth A],
L [auth A],
P [auth B],
R [auth C],
V [auth E],
W [auth E]
C3 H8 O3
Query on EDO

Download Ideal Coordinates CCD File 
N [auth A]1,2-ETHANEDIOL
C2 H6 O2
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSO
A, B, C, D, E
A, B, C, D, E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.968α = 82.15
b = 79.141β = 88.8
c = 95.47γ = 87.66
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

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