6FAN | pdb_00006fan

Crystal structure of putative CooT from Carboxydothermus hydrogenoformans

PDB DOI: https://doi.org/10.2210/pdb6FAN/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-12-15 Released: 2018-11-28
Deposition Author(s): Cavazza, C., Alfano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.275 (Depositor), 0.237 (DCC)
R-Value Work:
0.235 (Depositor), 0.238 (DCC)
R-Value Observed:
0.237 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Biophysical and structural characterization of the putative nickel chaperone CooT from Carboxydothermus hydrogenoformans.

Alfano, M., Perard, J., Miras, R., Catty, P., Cavazza, C.

(2018) J Biol Inorg Chem 23: 809-817

PubMed: 29882029 Search on PubMed
DOI: https://doi.org/10.1007/s00775-018-1576-2
Primary Citation Related Structures:
6FAN

PubMed Abstract:
Carboxydothermus hydrogenoformans is a model microorganism for the study of [NiFe]-CODH, a key enzyme of carbon cycle in anaerobic microorganisms. The enzyme possesses a unique active site (C-cluster), constituted of a distorted [NiFe ₃S ₄] cubane linked to a mononuclear Fe(II) center. Both the biogenesis of the C-cluster and the activation of CODH by nickel insertion remain unclear. Among the three accessory proteins thought to play a role in this latter step (CooC, CooJ, and CooT), CooT is identified as a nickel chaperone involved in CODH maturation in Rhodospirillum rubrum. Here, we structurally and biophysically characterized a putative CooT protein present in C. hydrogenoformans (pChCooT). Despite the low sequence homologies between CooT from R. rubrum (RrCooT) and pChCooT (19% sequence identity), the two proteins share several similarities, such as their overall structure and a solvent-exposed Ni(II)-binding site at the dimer interface. Moreover, the X-ray structure of pChCooT reveals the proximity between the histidine 55, a potential nickel-coordinating residue, and the cysteine 2, a highly conserved key residue in Ni(II)-binding.

Organizational Affiliation

University of Grenoble Alpes, CEA, CNRS, BIG, CBM, 38000, Grenoble, France.

Macromolecule Content

Total Structure Weight: 44.66 kDa
Atom Count: 3,093
Modeled Residue Count: 368
Deposited Residue Count: 378
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CooT	A, B, C, D, E A, B, C, D, E, F	63	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: CHY_0178
UniProt
Find proteins for Q3AFN4 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3AFN4 Go to UniProtKB: Q3AFN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3AFN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] MOL2 format, chain L [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] mmCIF format, chain L [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B]	G [auth B], J [auth C], K [auth D], L [auth E]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E] Interactions & Density Focus chain G [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain M [auth E] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain N [auth E] MOL2 format, chain M [auth E] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain N [auth E] mmCIF format, chain M [auth E] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B], M [auth E], N [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth E] Focus chain N [auth E] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth E] Focus chain N [auth E]