2EKQ

Structure of TT0495 protein from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The first crystal structure of NAD-dependent 3-dehydro-2-deoxy-D-gluconate dehydrogenase from Thermus thermophilus HB8

Pampa, K.J.Lokanath, N.K.Kunishima, N.Rai, R.V.

(2014) Acta Crystallogr D Biol Crystallogr 70: 994-1004

  • DOI: 10.1107/S1399004713034925
  • Primary Citation of Related Structures:  
    2EKP, 2EKQ, 4JP2, 4JP3

  • PubMed Abstract: 
  • 2-Keto-3-deoxygluconate (KDG) is one of the important intermediates in pectin metabolism. An enzyme involved in this pathway, 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (DDGDH), has been identified which converts 2,5-diketo-3-deoxygluconate to KDG. The enzyme is a member of the short-chain dehydrogenase (SDR) family ...

    2-Keto-3-deoxygluconate (KDG) is one of the important intermediates in pectin metabolism. An enzyme involved in this pathway, 3-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (DDGDH), has been identified which converts 2,5-diketo-3-deoxygluconate to KDG. The enzyme is a member of the short-chain dehydrogenase (SDR) family. To gain insight into the function of this enzyme at the molecular level, the first crystal structure of DDGDH from Thermus thermophilus HB8 has been determined in the apo form, as well as in complexes with the cofactor and with citrate, by X-ray diffraction methods. The crystal structures reveal a tight tetrameric oligomerization. The secondary-structural elements and catalytically important residues of the enzyme were highly conserved amongst the proteins of the NAD(P)-dependent SDR family. The DDGDH protomer contains a dinucleotide-binding fold which binds the coenzyme NAD(+) in an intersubunit cleft; hence, the observed oligomeric state might be important for the catalytic function. This enzyme prefers NAD(H) rather than NADP(H) as the physiological cofactor. A structural comparison of DDGDH with mouse lung carbonyl reductase suggests that a significant difference in the α-loop-α region of this enzyme is associated with the coenzyme specificity. The structural data allow a detailed understanding of the functional role of the conserved catalytic triad (Ser129-Tyr144-Lys148) in cofactor and substrate recognition, thus providing substantial insights into DDGDH catalysis. From analysis of the three-dimensional structure, intersubunit hydrophobic interactions were found to be important for enzyme oligomerization and thermostability.


    Organizational Affiliation

    Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore 570 006, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-deoxy-D-gluconate 3-dehydrogenaseA, B, C, D239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHB080
EC: 1.1.1.125
UniProt
Find proteins for Q53W82 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53W82 
Go to UniProtKB:  Q53W82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53W82
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.531α = 90
b = 110.531β = 90
c = 200.851γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2014-04-16
    Changes: Database references