5FIT

FHIT-SUBSTRATE ANALOG

• PDB DOI: https://doi.org/10.2210/pdb5FIT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-09-25 Released: 1998-03-25 
• Deposition Author(s): Lima, C.D., Klein, M.G., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Structure-based analysis of catalysis and substrate definition in the HIT protein family.

Lima, C.D., Klein, M.G., Hendrickson, W.A.

(1997) Science 278: 286-290

• PubMed: 9323207 
• DOI: https://doi.org/10.1126/science.278.5336.286
• Primary Citation of Related Structures:  
  1AV5, 1KPE, 1KPF, 4FIT, 5FIT, 6FIT


• PubMed Abstract: 
  

  The histidine triad (HIT) protein family is among the most ubiquitous and highly conserved in nature, but a biological activity has not yet been identified for any member of the HIT family. Fragile histidine triad protein (FHIT) and protein kinase C interacting protein (PKCI) were used in a structure-based approach to elucidate characteristics of in vivo ligands and reactions. Crystallographic structures of apo, substrate analog, pentacovalent transition-state analog, and product states of both enzymes reveal a catalytic mechanism and define substrate characteristics required for catalysis, thus unifying the HIT family as nucleotidyl hydrolases, transferases, or both. The approach described here may be useful in identifying structure-function relations between protein families identified through genomics.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.41 kDa 
• Atom Count: 1,081 
• Modelled Residue Count: 126 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FRAGILE HISTIDINE TRIAD PROTEIN	A	147	Homo sapiens	Mutation(s): 2  Gene Names: FHIT EC: 3.6.1.29 (PDB Primary Data), 3.6.2.1 (UniProt), 2.7.7.51 (UniProt), 3.9.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49789 (Homo sapiens) Explore P49789  Go to UniProtKB:  P49789
PHAROS:  P49789 GTEx:  ENSG00000189283

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP2	B [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C11 H17 N5 O9 P2 OLCWZBFDIYXLAA-IOSLPCCCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.258 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.64	α = 90
b = 50.64	β = 90
c = 267.52	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
XDS	data scaling
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-25 
Deposition Author(s): Lima, C.D., Klein, M.G., Hendrickson, W.A.

Revision History  

• Version 1.0: 1998-03-25
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other