4UOV | pdb_00004uov

The structure of a tetrameric alpha-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides, which contribute to its thermostability.

PDB DOI: https://doi.org/10.2210/pdb4UOV/pdb

Classification: LYASE
Organism(s): Thermovibrio ammonificans
Mutation(s): No

Deposited: 2014-06-10 Released: 2014-10-15
Deposition Author(s): James, P., Isupov, M., Sayer, C., Berg, S., Lioliou, M., Kotlar, H., Littlechild, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Structure of a Tetrameric [Alpha]-Carbonic Anhydrase from Thermovibrio Ammonificans Reveals a Core Formed Around Intermolecular Disulfides that Contribute to its Thermostability

James, P., Isupov, M.N., Sayer, C., Saneei, V., Berg, S., Lioliou, M., Kotlar, H., Littlechild, J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2607

PubMed: 25286845 Search on PubMed
DOI: https://doi.org/10.1107/S1399004714016526
Primary Citation Related Structures:
4C3T, 4COQ, 4UOV

PubMed Abstract:
Carbonic anhydrase enzymes catalyse the reversible hydration of carbon dioxide to bicarbonate. A thermophilic Thermovibrio ammonificans α-carbonic anhydrase (TaCA) has been expressed in Escherichia coli and structurally and biochemically characterized. The crystal structure of TaCA has been determined in its native form and in two complexes with bound inhibitors. The tetrameric enzyme is stabilized by a unique core in the centre of the molecule formed by two intersubunit disulfides and a single lysine residue from each monomer that is involved in intersubunit ionic interactions. The structure of this core protects the intersubunit disulfides from reduction, whereas the conserved intrasubunit disulfides are not formed in the reducing environment of the E. coli host cytosol. When oxidized to mimic the environment of the periplasmic space, TaCA has increased thermostability, retaining 90% activity after incubation at 70°C for 1 h, making it a good candidate for industrial carbon-dioxide capture. The reduction of all TaCA cysteines resulted in dissociation of the tetrameric molecule into monomers with lower activity and reduced thermostability. Unlike other characterized α-carbonic anhydrases, TaCA does not display esterase activity towards p-nitrophenyl acetate, which appears to result from the increased rigidity of its protein scaffold.

Organizational Affiliation

Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England.

Macromolecule Content

Total Structure Weight: 174.73 kDa
Atom Count: 14,247
Modeled Residue Count: 1,350
Deposited Residue Count: 1,482
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONATE DEHYDRATASE	A, B, C, D, E A, B, C, D, E, F	247	Thermovibrio ammonificans	Mutation(s): 0 EC: 4.2.1.1
UniProt
Find proteins for E8T502 (Thermovibrio ammonificans (strain DSM 15698 / JCM 12110 / HB-1)) Explore E8T502 Go to UniProtKB: E8T502
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E8T502
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain DB [auth F] SDF format, chain I [auth A] SDF format, chain S [auth B] MOL2 format, chain DB [auth F] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] mmCIF format, chain DB [auth F] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B]	DB [auth F], I [auth A], S [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain DB [auth F] Focus chain I [auth A] Focus chain S [auth B] Interactions & Density Focus chain DB [auth F] Focus chain I [auth A] Focus chain S [auth B]
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain EB [auth F] SDF format, chain NA [auth D] SDF format, chain UA [auth E] SDF format, chain J [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth F] MOL2 format, chain NA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain J [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain EB [auth F] mmCIF format, chain NA [auth D] mmCIF format, chain UA [auth E] mmCIF format, chain J [auth A]	EA [auth C], EB [auth F], J [auth A], NA [auth D], UA [auth E]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain EB [auth F] Focus chain J [auth A] Focus chain NA [auth D] Focus chain UA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain EB [auth F] Focus chain J [auth A] Focus chain NA [auth D] Focus chain UA [auth E]
AZM Query on AZM Download:Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain DA [auth C] SDF format, chain H [auth A] SDF format, chain MA [auth D] SDF format, chain R [auth B] SDF format, chain TA [auth E] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain TA [auth E] mmCIF format, chain CB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain TA [auth E]	CB [auth F] DA [auth C] H [auth A] MA [auth D] R [auth B] CB [auth F], DA [auth C], H [auth A], MA [auth D], R [auth B], TA [auth E]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C₄ H₆ N₄ O₃ S₂ BZKPWHYZMXOIDC-UHFFFAOYSA-N		Interactions Focus chain CB [auth F] Focus chain DA [auth C] Focus chain H [auth A] Focus chain MA [auth D] Focus chain R [auth B] Focus chain TA [auth E] Interactions & Density Focus chain CB [auth F] Focus chain DA [auth C] Focus chain H [auth A] Focus chain MA [auth D] Focus chain R [auth B] Focus chain TA [auth E]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain JB [auth F] SDF format, chain QA [auth D] SDF format, chain W [auth B] SDF format, chain XA [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain JB [auth F] MOL2 format, chain QA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain XA [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain JB [auth F] mmCIF format, chain QA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain XA [auth E]	IA [auth C], JB [auth F], QA [auth D], W [auth B], XA [auth E]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain JB [auth F] Focus chain QA [auth D] Focus chain W [auth B] Focus chain XA [auth E] Interactions & Density Focus chain IA [auth C] Focus chain JB [auth F] Focus chain QA [auth D] Focus chain W [auth B] Focus chain XA [auth E]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain HB [auth F] SDF format, chain X [auth B] SDF format, chain O [auth A] MOL2 format, chain HB [auth F] MOL2 format, chain X [auth B] MOL2 format, chain O [auth A] mmCIF format, chain HB [auth F] mmCIF format, chain X [auth B] mmCIF format, chain O [auth A]	HB [auth F], O [auth A], X [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain HB [auth F] Focus chain O [auth A] Focus chain X [auth B] Interactions & Density Focus chain HB [auth F] Focus chain O [auth A] Focus chain X [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain KA [auth C] SDF format, chain KB [auth F] SDF format, chain LB [auth F] SDF format, chain N [auth A] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] SDF format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth F] MOL2 format, chain LB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth F] mmCIF format, chain LB [auth F] mmCIF format, chain N [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain AB [auth E]	AB [auth E] BA [auth B] KA [auth C] KB [auth F] LB [auth F] AB [auth E], BA [auth B], KA [auth C], KB [auth F], LB [auth F], N [auth A], Z [auth B], ZA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain N [auth A] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BA [auth B] Focus chain KA [auth C] Focus chain KB [auth F] Focus chain LB [auth F] Focus chain N [auth A] Focus chain Z [auth B] Focus chain ZA [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain FB [auth F] SDF format, chain OA [auth D] SDF format, chain VA [auth E] SDF format, chain T [auth B] SDF format, chain K [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth F] MOL2 format, chain OA [auth D] MOL2 format, chain VA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth F] mmCIF format, chain OA [auth D] mmCIF format, chain VA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A]	FA [auth C] FB [auth F] K [auth A] OA [auth D] T [auth B] FA [auth C], FB [auth F], K [auth A], OA [auth D], T [auth B], VA [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth C] Focus chain FB [auth F] Focus chain K [auth A] Focus chain OA [auth D] Focus chain T [auth B] Focus chain VA [auth E] Interactions & Density Focus chain FA [auth C] Focus chain FB [auth F] Focus chain K [auth A] Focus chain OA [auth D] Focus chain T [auth B] Focus chain VA [auth E]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain CA [auth C] SDF format, chain G [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] SDF format, chain SA [auth E] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth E] mmCIF format, chain BB [auth F] mmCIF format, chain CA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain SA [auth E]	BB [auth F] CA [auth C] G [auth A] LA [auth D] Q [auth B] BB [auth F], CA [auth C], G [auth A], LA [auth D], Q [auth B], SA [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain CA [auth C] Focus chain G [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain SA [auth E] Interactions & Density Focus chain BB [auth F] Focus chain CA [auth C] Focus chain G [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Focus chain SA [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain GB [auth F] SDF format, chain HA [auth C] SDF format, chain IB [auth F] SDF format, chain JA [auth C] SDF format, chain M [auth A] SDF format, chain PA [auth D] SDF format, chain RA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain WA [auth E] SDF format, chain YA [auth E] SDF format, chain Y [auth B] SDF format, chain P [auth A] SDF format, chain L [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth F] MOL2 format, chain HA [auth C] MOL2 format, chain IB [auth F] MOL2 format, chain JA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain YA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain P [auth A] MOL2 format, chain L [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth F] mmCIF format, chain HA [auth C] mmCIF format, chain IB [auth F] mmCIF format, chain JA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain YA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain P [auth A] mmCIF format, chain L [auth A]	GA [auth C] GB [auth F] HA [auth C] IB [auth F] JA [auth C] GA [auth C], GB [auth F], HA [auth C], IB [auth F], JA [auth C], L [auth A], M [auth A], P [auth A], PA [auth D], RA [auth D], U [auth B], V [auth B], WA [auth E], Y [auth B], YA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain IB [auth F] Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Interactions & Density Focus chain GA [auth C] Focus chain GB [auth F] Focus chain HA [auth C] Focus chain IB [auth F] Focus chain JA [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth A] Focus chain PA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain YA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.204 (Depositor), 0.204 (DCC)
R-Value Work: 0.172 (Depositor), 0.172 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.75	α = 90
b = 283.02	β = 90
c = 52.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary