3TTB | pdb_00003ttb

Structure of the Thioalkalivibrio paradoxus cytochrome c nitrite reductase in complex with sulfite

PDB DOI: https://doi.org/10.2210/pdb3TTB/pdb

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

Deposited: 2011-09-14 Released: 2011-10-05
Deposition Author(s): Polyakov, K.M., Trofimov, A.A., Tikhonova, T.V., Tikhonov, A.V., Dorovatovskii, P.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.153 (Depositor), 0.127 (DCC)
R-Value Work:
0.134 (Depositor), 0.126 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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 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. Nucleotide sequence data are available in the GenBank database under the accession number HQ665012.1. Structural data are available in the RCSB Protein Data Bank database under the accession numbers 3SXQ and 3TTB STRUCTURED DIGITAL ABSTRACT: TvPaR and TvPaR bind by x-ray crystallography (View interaction).

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 129.96 kDa
Atom Count: 9,727
Modeled Residue Count: 1,040
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eight-heme nitrite reductase	A, B	525	Thioalkalivibrio paradoxus	Mutation(s): 0 EC: 1.7.2.2
UniProt
Find proteins for E7EDQ7 (Thioalkalivibrio paradoxus) Explore E7EDQ7 Go to UniProtKB: E7EDQ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E7EDQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 D [auth A] 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 U [auth B] SDF format, chain V [auth B] 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 D [auth A] 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 U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] C [auth A] D [auth A] E [auth A] AA [auth B], BA [auth B], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], U [auth B], V [auth B], 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 D [auth A] 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 U [auth B] Focus chain V [auth B] 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 D [auth A] 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 U [auth B] Focus chain V [auth B] 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 LA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	JA [auth B] KA [auth B] LA [auth B] Q [auth A] R [auth A] JA [auth B], KA [auth B], LA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	GA [auth B], HA [auth B], IA [auth B], O [auth A], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain O [auth A] Focus chain P [auth A]
SO3 Query on SO3 Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain K [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain K [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain K [auth A]	CA [auth B], K [auth A]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain K [auth A] Interactions & Density Focus chain CA [auth B] Focus chain K [auth A]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	EA [auth B], FA [auth B], M [auth A], N [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain M [auth A] Focus chain N [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain L [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain L [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain L [auth A]	DA [auth B], L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain L [auth A] Interactions & Density Focus chain DA [auth B] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.153 (Depositor), 0.127 (DCC)
R-Value Work: 0.134 (Depositor), 0.126 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.99	α = 90
b = 190.99	β = 90
c = 190.99	γ = 90

Software Package:

Software Name	Purpose
AUTOMAR	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2012-09-26
Changes: Database references
Version 1.2: 2012-12-19
Changes: Database references
Version 1.3: 2019-11-20
Changes: Advisory, Derived calculations
Version 1.4: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-27
Changes: Structure summary