Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 110.73 kDa 
• Atom Count: 8487 
• Residue Count: 988 
• Unique protein chains: 1

1RZQ

Crystal Structure of C-Terminal Despentapeptide Nitrite Reductase from Achromobacter Cycloclastes at pH5.0

• DOI: 10.2210/pdb1RZQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Achromobacter cycloclastes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-26 Released: 2004-03-30 
• Deposition Author(s): Li, H.T., Wang, C., Chang, T., Chang, W.C., Liu, M.Y., Le Gall, J., Gui, L.L., Zhang, J.P., An, X.M., Chang, W.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.208 
• R-Value Work: 0.181 

Literature

pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes

Li, H.T., Wang, C., Chang, T., Chang, W.C., Liu, M.Y., Le Gall, J., Gui, L.L., Zhang, J.P., An, X.M., Chang, W.R.

(2004) Biochem Biophys Res Commun 316: 107-113

• PubMed: 15003518 
• DOI: 10.1016/j.bbrc.2004.01.177
• Primary Citation of Related Structures:  
  1RZP, 1RZQ


• PubMed Abstract: 
  

Crystal structures of C-terminal despentapeptide nitrite reductase (NiRc-5) from Achromobacter cycloclastes were determined from 1.9 to 2.3A at pH 5.0, 5.4, and 6.2. NiRc-5, that has lost about 30% activity, is found to possess quite similar trimeric structures as the native enzyme. Electron density and copper content measurements indicate that the activity loss is not caused by the release of type 2 copper (T2Cu). pH-profile structural comparisons with native enzyme reveal that the T2Cu active center in NiRc-5 is perturbed, accounting for the partial loss of enzyme activity. This perturbation likely results from the less constrained conformations of two catalytic residues, Asp98 and His255. Hydrogen bonding analysis shows that the deletion of five residues causes a loss of more than half the intersubunit hydrogen bonds mediated by C-terminal tail. This study shows that the C-terminal tail plays an important role in controlling the conformations around the T2Cu site at the subunit interface, and helps keep the optimum microenvironment of active center for the full enzyme activity of AcNiR.

---

Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15th Datun Road, Chaoyang District, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	335	Achromobacter cycloclastes	Mutation(s): 0  Gene Names: nirK EC: 1.7.2.1
Find proteins for P25006 (Achromobacter cycloclastes) Explore P25006  Go to UniProtKB:  P25006

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU	A, B, C	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACY	A, C	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.208 
• R-Value Work: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.02	α = 90
b = 117.44	β = 90
c = 122.8	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-26 
• Released Date: 2004-03-30 
Deposition Author(s): Li, H.T., Wang, C., Chang, T., Chang, W.C., Liu, M.Y., Le Gall, J., Gui, L.L., Zhang, J.P., An, X.M., Chang, W.R.

Revision History 

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance