2GRU

Crystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and Co2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+

Nango, E.Kumasaka, T.Hirayama, T.Tanaka, N.Eguchi, T.

(2008) Proteins 70: 517-527

  • DOI: 10.1002/prot.21526
  • Primary Citation of Related Structures:  
    2GRU, 2D2X

  • PubMed Abstract: 
  • A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization ...

    A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose-6-phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N-terminal and C-terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn-elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism.


    Organizational Affiliation

    Department of Chemistry, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-deoxy-scyllo-inosose synthaseA, B368Bacillus circulansMutation(s): 0 
Gene Names: btrC
EC: 4.2.3 (PDB Primary Data), 4.2.3.124 (UniProt)
Find proteins for Q9S5E2 (Bacillus circulans)
Explore Q9S5E2 
Go to UniProtKB:  Q9S5E2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
F [auth A], K [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
CAK
Query on CAK

Download Ideal Coordinates CCD File 
L [auth B][(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE
C7 H15 O8 P
FPLZFJHCPYNBEO-OVHBTUCOSA-N
 Ligand Interaction
EXO
Query on EXO

Download Ideal Coordinates CCD File 
G [auth A](1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL
C7 H12 O4
DRZDCPGIBPDBFY-JWXFUTCRSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth A], M [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO3
Query on SO3

Download Ideal Coordinates CCD File 
D [auth A], J [auth B]SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
C [auth A], I [auth B]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.569α = 90
b = 70.108β = 117.61
c = 81.569γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
XFITdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-04-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance