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 PISA (software)

Macromolecule Content

• Total Structure Weight: 169.17 kDa 
• Atom Count: 12600 
• Modelled Residue Count: 1438 
• Deposited Residue Count: 1438 
• Unique protein chains: 1

1Z68

Crystal Structure Of Human Fibroblast Activation Protein alpha

• DOI: 10.2210/pdb1Z68/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-03-21 Released: 2005-04-12 
• Deposition Author(s): Aertgeerts, K., Levin, I., Shi, L., Prasad, G.S., Zhang, Y., Kraus, M.L., Salakian, S., Snell, G.P., Sridhar, V., Wijnands, R., Tennant, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.283 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Structural and kinetic analysis of the substrate specificity of human fibroblast activation protein alpha.

Aertgeerts, K., Levin, I., Shi, L., Snell, G.P., Jennings, A., Prasad, G.S., Zhang, Y., Kraus, M.L., Salakian, S., Sridhar, V., Wijnands, R., Tennant, M.G.

(2005) J Biol Chem 280: 19441-19444

• PubMed: 15809306 
• DOI: 10.1074/jbc.C500092200
• Primary Citation of Related Structures:  
  1Z68


• PubMed Abstract: 
  

Fibroblast activation protein alpha (FAPalpha) is highly expressed in epithelial cancers and has been implicated in extracellular matrix remodeling, tumor growth, and metastasis. We present the first high resolution structure for the apoenzyme as well as kinetic data toward small dipeptide substrates. FAPalpha exhibits a dipeptidyl peptidase IV (DPPIV)-like fold, featuring an alpha/beta-hydrolase domain and an eight-bladed beta-propeller domain. Known DPPIV dipeptides are cleaved by FAPalpha with an approximately 100-fold decrease in catalytic efficiency compared with DPPIV. Moreover, FAPalpha, but not DPPIV, possesses endopeptidase activity toward N-terminal benzyloxycarbonyl (Z)-blocked peptides. Comparison of the crystal structures of FAPalpha and DPPIV revealed one major difference in the vicinity of the Glu motif (Glu(203)-Glu(204) for FAPalpha; Glu(205)-Glu(206) for DPPIV) within the active site of the enzyme. Ala(657) in FAPalpha, instead of Asp(663) as in DP-PIV, reduces the acidity in this pocket, and this change could explain the lower affinity for N-terminal amines by FAPalpha. This hypothesis was tested by kinetic analysis of the mutant FAPalpha/A657D, which shows on average an approximately 60-fold increase in the catalytic efficiency, as measured by k(cat)/K(m), for the cleavage of dipeptide substrates. Furthermore, the catalytic efficiency of the mutant is reduced by approximately 350-fold for cleavage of Z-Gly-Pro-7-amino-4-methylcoumarin. Our data provide a clear understanding of the molecular determinants responsible for the substrate specificity and endopeptidase activity of FAPalpha.

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Organizational Affiliation: 

Takeda San Diego, Inc., California 92121, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fibroblast activation protein, alpha subunit	A, B	719	Homo sapiens	Mutation(s): 0  Gene Names: FAP EC: 3.4.21 (PDB Primary Data), 3.4.21.26 (UniProt), 3.4.14.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q12884 (Homo sapiens) Explore Q12884  Go to UniProtKB:  Q12884
PHAROS:  Q12884 GTEx:  ENSG00000078098

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79924RM GlyCosmos:  G79924RM GlyGen:  G79924RM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.283 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.295	α = 90
b = 152.58	β = 90
c = 214.855	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-03-21 
• Released Date: 2005-04-12 
Deposition Author(s): Aertgeerts, K., Levin, I., Shi, L., Prasad, G.S., Zhang, Y., Kraus, M.L., Salakian, S., Snell, G.P., Sridhar, V., Wijnands, R., Tennant, M.G.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary