Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 68.66 kDa 
• Atom Count: 4908 
• Modelled Residue Count: 622 
• Deposited Residue Count: 631 
• Unique protein chains: 2

3E8L

The Crystal Structure of the Double-headed Arrowhead Protease Inhibitor A in Complex with Two Trypsins

• DOI: 10.2210/pdb3E8L/pdb

• Classification: HYDROLASE INHIBITOR/HYDROLASE
• Organism(s): Sagittaria sagittifolia, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-08-20 Released: 2009-07-28 
• Deposition Author(s): Bao, R., Jiang, C.-H., Chi, C.W., Lin, S.X., Chen, Y.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.245 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

The ternary structure of double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation.

Bao, R., Zhou, C.Z., Jiang, C.-H., Lin, S.X., Chi, C.W., Chen, Y.X.

(2009) J Biol Chem 284: 26676-26684

• PubMed: 19640842 
• DOI: 10.1074/jbc.M109.022095
• Primary Citation of Related Structures:  
  3E8L


• PubMed Abstract: 
  

The double-headed arrowhead protease inhibitors API-A and -B from the tubers of Sagittaria sagittifolia (Linn) feature two distinct reactive sites, unlike other members of their family. Although the two inhibitors have been extensively characterized, the identities of the two P1 residues in both API-A and -B remain controversial. The crystal structure of a ternary complex at 2.48 A resolution revealed that the two trypsins bind on opposite sides of API-A and are 34 A apart. The overall fold of API-A belongs to the beta-trefoil fold and resembles that of the soybean Kunitz-type trypsin inhibitors. The two P1 residues were unambiguously assigned as Leu(87) and Lys(145), and their identities were further confirmed by site-directed mutagenesis. Reactive site 1, composed of residues P5 Met(83) to P5' Ala(92), adopts a novel conformation with the Leu(87) completely embedded in the S1 pocket even though it is an unfavorable P1 residue for trypsin. Reactive site 2, consisting of residues P5 Cys(141) to P5' Glu(150), binds trypsin in the classic mode by employing a two-disulfide-bonded loop. Analysis of the two binding interfaces sheds light on atomic details of the inhibitor specificity and also promises potential improvements in enzyme activity by engineering of the reactive sites.

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Organizational Affiliation: 

Institute of Protein Research, Tongji University, Shanghai, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine proteinase inhibitor A	A [auth C]	185	Sagittaria sagittifolia	Mutation(s): 2
Find proteins for Q7M1P4 (Sagittaria sagittifolia) Explore Q7M1P4  Go to UniProtKB:  Q7M1P4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	B [auth A], C [auth B]	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	DA [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	I [auth C], U [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth C], E [auth C], F [auth C], R [auth A], S [auth A], T [auth A], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], CA [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	EA [auth B], G [auth C], H [auth C], V [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A], W [auth B], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	J [auth A], K [auth A], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.245 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.634	α = 90
b = 110.863	β = 90
c = 152.991	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
SCALA	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-20 
• Released Date: 2009-07-28 
Deposition Author(s): Bao, R., Jiang, C.-H., Chi, C.W., Lin, S.X., Chen, Y.X.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2013-09-18
  Changes: Database references, Derived calculations