Crystal structure of E55Q mutant of nitrophorin 4

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Effect of mutation of carboxyl side-chain amino acids near the heme on the midpoint potentials and ligand binding constants of nitrophorin 2 and its NO, histamine, and imidazole complexes.

Berry, R.E.Shokhirev, M.N.Ho, A.Y.Yang, F.Shokhireva, T.K.Zhang, H.Weichsel, A.Montfort, W.R.Walker, F.A.

(2009) J Am Chem Soc 131: 2313-2327

  • DOI: https://doi.org/10.1021/ja808105d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Nitrophorins (NPs) are a group of NO-carrying heme proteins found in the saliva of a blood-sucking insect from tropical Central and South America, Rhodnius prolixus, the "kissing bug". NO is kept stable for long periods of time by binding it as an axial ligand to a ferriheme center. The fact that the nitrophorins are stabilized as Fe(III)-NO proteins is a unique property because most heme proteins are readily autoreduced by excess NO and bind NO to the Fe(II) heme irreversibly (K(d)s in the picomolar range). In contrast, the nitrophorins, as Fe(III) heme centers, have K(d)s in the micromolar to nanomolar range and thus allow NO to dissociate upon dilution following injection into the tissues of the victim. This NO can cause vasodilation and thereby allow more blood to be transported to the site of the wound. We prepared 13 site-directed mutants of three major nitrophorins, NP2, NP1, and NP4, to investigate the stabilization of the ferric-NO heme center and preservation of reversible binding that facilitates these proteins' NO storage, transport, and release functions. Of the mutations in which Glu and/or Asp were replaced by Ala, most of these carboxyls show a significant role stabilizing Fe(III)-NO over Fe(II)-NO, with buried E53 of NP2 or E55 of NP1 and NP4 being the most important and partially buried D29 of NP2 or D30 of NP4 being second in importance. The pK(a)s of the carboxyl groups studied vary significantly but all are largely deprotonated at pH 7.5 except E124.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, The University of Arizona, P.O. Box 210041, Tucson, Arizona 85721-0041, USA. berryr@email.arizona.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrophorin-4184Rhodnius prolixusMutation(s): 1 
Find proteins for Q94734 (Rhodnius prolixus)
Explore Q94734 
Go to UniProtKB:  Q94734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94734
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
C34 H32 Fe N4 O4
Query on NH3

Download Ideal Coordinates CCD File 
H3 N
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.379α = 90
b = 42.838β = 94.2
c = 53.056γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description