3SXQ

Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio paradoxus

PDB DOI: https://doi.org/10.2210/pdb3SXQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thioalkalivibrio paradoxus
Mutation(s): No

Deposited: 2011-07-15 Released: 2012-09-26
Deposition Author(s): Polyakov, K.M., Trofimov, A.A., Tikhonova, T.V., Tikhonov, A.V., Boyko, K.M., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.162
R-Value Work: 0.138
R-Value Observed: 0.139

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species.

Tikhonova, T., Tikhonov, A., Trofimov, A., Polyakov, K., Boyko, K., Cherkashin, E., Rakitina, T., Sorokin, D., Popov, V.

(2012) FEBS J 279: 4052-4061

PubMed: 22935005 Search on PubMed
DOI: https://doi.org/10.1111/j.1742-4658.2012.08811.x
Primary Citation of Related Structures:
3SXQ, 3TTB

PubMed Abstract:
Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic properties, owing to high structural similarity. Both enzymes are characterized by specific structural features distinguishing them from pentaheme cytochrome c nitrite reductases, such as the Tyr-Cys bond in the active site, the hexameric structure resulting in the formation of a void space inside the hexamer, and the product channel that opens into the void interior space of the hexamer. It is suggested that these specific structural features are responsible for the higher nitrite reductase activity, the greater preference for nitrite than for sulfite as a substrate, and the wider pH range of the catalytic activity of octaheme nitrite reductases than of pentaheme homologs.

Organizational Affiliation

Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia. ttikhonova@inbi.ras.ru

Macromolecule Content

Total Structure Weight: 129.91 kDa
Atom Count: 10,297
Modelled Residue Count: 1,037
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eight-heme nitrite reductase	A, B	525	Thioalkalivibrio paradoxus	Mutation(s): 0
UniProt
Find proteins for E7EDQ7 (Thioalkalivibrio paradoxus) Explore E7EDQ7 Go to UniProtKB: E7EDQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E7EDQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	JA [auth B], KA [auth B], P [auth A], Q [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain P [auth A] Focus chain Q [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A]	LA [auth B] MA [auth B] NA [auth B] R [auth A] S [auth A] LA [auth B], MA [auth B], NA [auth B], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	FA [auth B], GA [auth B], L [auth A], M [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain L [auth A] Focus chain M [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain K [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain K [auth A]	EA [auth B], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain K [auth A] Interactions & Density Focus chain EA [auth B] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain O [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain O [auth A]	IA [auth B], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain IA [auth B] Focus chain O [auth A] Interactions & Density Focus chain IA [auth B] Focus chain O [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain N [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain N [auth A]	HA [auth B], N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain N [auth A] Interactions & Density Focus chain HA [auth B] Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.162
R-Value Work: 0.138
R-Value Observed: 0.139
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.64	α = 90
b = 193.64	β = 90
c = 193.64	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2012-12-19
Changes: Database references
Version 1.2: 2019-11-20
Changes: Advisory, Derived calculations
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description