Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.89 kDa 
• Atom Count: 1050 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

1CUO

CRYSTAL STRUCTURE ANALYSIS OF ISOMER-2 AZURIN FROM METHYLOMONAS J

• DOI: 10.2210/pdb1CUO/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Methylomonas sp. J
• Mutation(s): No 


• Deposited: 1999-08-21 Released: 2000-08-23 
• Deposition Author(s): Inoue, T., Nishio, N., Kai, Y., Suzuki, S., Kataoka, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.242 
• R-Value Work: 0.175 
• R-Value Observed: 0.184 

Literature

The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J.

Inoue, T., Suzuki, S., Nishio, N., Yamaguchi, K., Kataoka, K., Tobari, J., Yong, X., Hamanaka, S., Matsumura, H., Kai, Y.

(2003) J Mol Biol 333: 117-124

• PubMed: 14516747 
• DOI: 10.1016/j.jmb.2003.08.002
• Primary Citation of Related Structures:  
  1CUO, 1UAT


• PubMed Abstract: 
  

The obligate methylotroph Methylomonas sp. strain J produces two azurins (Az-iso1 and Az-iso2) as candidates for electron acceptor from methylamine dehydrogenase (MADH) in the electron-transfer process involving the oxidation of methylamine to formaldehyde and ammonia. The X-ray crystallographic study indicated that Az-iso2 gives two types of crystals (form I and form II) with polyethylene glycol (PEG4000) and ammonium sulfate as the precipitants, respectively. Comparison between the two Az-iso2 structures in forms I and II reveals the remarkable structural changes at the top surface of the molecule around the copper atom. Az-iso2 possesses Gly43 instead of Val43 or Ala43, which is unique among all other azurins around the copper ligand His46, inducing the remarkable structural change in the loop region from Gly37 to Gly43. When the structure of Az-iso2 is superimposed on that of amicyanin in the ternary complex composed of MADH, amicyanin, and cytochrome c(551), the loop of Az-iso2 deeply overlaps with the light subunit of MADH. However, the Az-iso2 molecule is probably able to avoid any steric hindrance with the cognate MADH to form the complex for intermolecular electron-transfer reaction, since the loop containing Gly43 is flexible. We discuss why the electron-transfer activity of Az-iso2 is fivefold higher than that of Az-iso1.

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Related Citations: 

• Two distinct azurins function in the electron-transport chain of the obligate methylotroph Methylomonas J
  Ambler, R.P., Tobari, J.
  (1989) Biochem J 261: 495

• Crystallization and preliminary X-ray study of iso-2 azurin from the methylotrophic bacterium, Methylomonas J
  Inoue, T., Nishio, N., Kai, Y., Suzuki, S., Kataoka, K.
  (1999) Acta Crystallogr D Biol Crystallogr 55: 307

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Organizational Affiliation: 

Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (AZURIN ISO-2)	A	129	Methylomonas sp. J	Mutation(s): 0
Find proteins for P12335 (Methylomonas sp. (strain J)) Explore P12335  Go to UniProtKB:  P12335

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.242 
• R-Value Work: 0.175 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.96	α = 90
b = 33.67	β = 101.35
c = 47.34	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-08-21 
• Released Date: 2000-08-23 
Deposition Author(s): Inoue, T., Nishio, N., Kai, Y., Suzuki, S., Kataoka, K.

Revision History  

• Version 1.0: 2000-08-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance