1P77 | pdb_00001p77

CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) FROM HAEMOPHILUS INFLUENZAE

• PDB DOI: https://doi.org/10.2210/pdb1P77/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-04-30 Released: 2003-08-12 
• Deposition Author(s): Ye, S., von Delft, F., Brooun, A., Knuth, M.W., Swanson, R.V., McRee, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.244 (Depositor) 
• R-Value Work: 
  0.203 (Depositor) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of shikimate dehydrogenase (AroE) reveals a unique NADPH binding mode

Ye, S., von Delft, F., Brooun, A., Knuth, M.W., Swanson, R.V., McRee, D.E.

(2003) J Bacteriol 185: 4144-4151

• PubMed: 12837789 
• DOI: https://doi.org/10.1128/JB.185.14.4144-4151.2003
• Primary Citation Related Structures: 
  1P74, 1P77


• PubMed Abstract: 
  

  Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from Haemophilus influenzae to 2.4-A resolution and its complex with NADPH to 1.95-A resolution. The molecule contains two domains, a catalytic domain with a novel open twisted alpha/beta motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.

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Organizational Affiliation: 
• Syrrx Inc., San Diego, California 92121, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.35 kDa 
• Atom Count: 2,347 
• Modeled Residue Count: 265 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate 5-dehydrogenase	A	272	Haemophilus influenzae	Mutation(s): 0  Gene Names: AROE OR HI0655 EC: 1.1.1.25
UniProt
Find proteins for P43876 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P43876  Go to UniProtKB:  P43876

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATR	C [auth A]	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE C10 H16 N5 O13 P3 YPTPYQSAVGGMFN-KQYNXXCUSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.244 (Depositor) 
• R-Value Work:  0.203 (Depositor) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.054	α = 90
b = 82.728	β = 90
c = 82.365	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-12 
Deposition Author(s): Ye, S., von Delft, F., Brooun, A., Knuth, M.W., Swanson, R.V., McRee, D.E.

Revision History  

• Version 1.0: 2003-08-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Database references
• Version 2.0: 2023-08-16
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description