Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 80.65 kDa 
• Atom Count: 6465 
• Residue Count: 693 
• Unique protein chains: 1

1OC2

The structure of NADH in the dTDP-D-glucose dehydratase (RmlB) enzyme

• DOI: 10.2210/pdb1OC2/pdb

• Classification: LYASE
• Organism(s): Streptococcus suis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-02-04 Released: 2003-10-02 
• Deposition Author(s): Beis, K., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

The Structure of Nadh in the Enzyme Dtdp-D-Glucose Dehydratase (Rmlb)

Beis, K., Allard, S.T., Hegeman, A.D., Murshudov, G., Philp, D., Naismith, J.H.

(2003) J Am Chem Soc 125: 11872

• PubMed: 14505409 
• DOI: 10.1021/ja035796r
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The structure of Streptococcus suis serotype type 2 dTDP-d-glucose 4,6-dehydratase (RmlB) has been determined to 1.5 A resolution with its nicotinamide coenzyme and substrate analogue dTDP-xylose bound in an abortive complex. During enzyme turnover, NAD(+) abstracts a hydride from the C4' atom of dTDP-glucose-forming NADH. After elimination of water, hydride is then transferred back to the C6' atom of dTDP-4-keto-5,6-glucosene-regenerating NAD(+). Single-crystal spectroscopic studies unambiguously show that the coenzyme has been trapped as NADH in the crystal. Electron density clearly demonstrates that in contrast to native structures of RmlB where a flat nicotinamide ring is observed, the dihydropyridine ring of the reduced cofactor in this complex is found as a boat. The si face, from which the pro-S hydride is transferred, has a concave surface. Ab initio electronic structure calculations demonstrate that the presence of an internal hydrogen bond, between the amide NH on the nicotinamide ring and one of the oxygen atoms on a phosphate group, stabilizes this distorted conformation. Additionally, calculations show that the hydride donor ability of NADH is influenced by the degree of bending in the ring and may be influenced by an active-site tyrosine residue (Tyr 161). These results demonstrate the ability of dehydratase enzymes to fine-tune the redox potential of NADH through conformational changes in the nicotinamide ring.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DTDP-GLUCOSE 4,6-DEHYDRATASE	A, B	348	Streptococcus suis	Mutation(s): 0  Gene Names:  rmlB, rfbB, A6M16_03315, APQ97_03200, CWI26_07360, CWM22_07885, E8M06_06710, EI219_02305, ERS132370_01395, ERS132374_01253, ERS132410_01682, ERS132414_00580, ERS132421_00412, ERS132431_00441, ERS132440_01438, ERS132444_01827, ERS132457_01850, ERS132458_00971, ERS132461_00211, ERS132462_01604, ERS132502_01610, ERS132531_00495, ERS132536_02274, FAJ39_02870, FH692_06610, GNK10_04820, LI88_04195 EC: 4.2.1.46
Find proteins for Q8GIP9 (Streptococcus suis) Go to UniProtKB:  Q8GIP9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	A, B	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
TDX	A, B	THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE C15 H24 N2 O15 P2 AJUADKZRQSBUAK-KDGZBOQCSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.41	α = 90
b = 94.829	β = 90
c = 183.543	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-04 
• Released Date: 2003-10-02 
Deposition Author(s): Beis, K., Naismith, J.H.

Revision History 

• Version 1.0: 2003-10-02
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Source and taxonomy