1PC5 | pdb_00001pc5

Crystal Structure of the P50G Mutant of Ferredoxin I at 1.8 A Resolution

PDB DOI: https://doi.org/10.2210/pdb1PC5/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Azotobacter vinelandii
Expression System: Azotobacter vinelandii
Mutation(s): Yes

Deposited: 2003-05-15 Released: 2003-09-30
Deposition Author(s): Camba, R., Jung, Y.S., Chen, K., Hunsicker-Wang, L.M., Burgess, B.K., Stout, C.D., Hirst, J., Armstrong, F.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.253 (Depositor)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Mechanisms of redox-coupled proton transfer in proteins: role of the proximal proline in reactions of the [3Fe-4S] cluster in Azotobacter vinelandii ferredoxin I

Camba, R., Jung, Y.S., Hunsicker-Wang, L.M., Burgess, B.K., Stout, C.D., Hirst, J., Armstrong, F.A.

(2003) Biochemistry 42: 10589-10599

PubMed: 12962482 Search on PubMed
DOI: https://doi.org/10.1021/bi035021v
Primary Citation Related Structures:
1PC4, 1PC5

PubMed Abstract:
The 7Fe ferredoxin from Azotobacter vinelandii (AvFdI) contains a [3Fe-4S](+/0) cluster that binds a single proton in its reduced level. Although the cluster is buried, and therefore inaccessible to solvent, proton transfer from solvent to the cluster is fast. The kinetics and energetics of the coupled electron-proton transfer reaction at the cluster have been analyzed in detail by protein-film voltammetry, to reveal that proton transfer is mediated by the mobile carboxylate of an adjacent surface residue, aspartate-15, the pK of which is sensitive to the charge on the cluster. This paper examines the role of a nearby proline residue, proline-50, in proton transfer and its coupling to electron transfer. In the P50A and P50G mutants, a water molecule has entered the cluster binding region; it is hydrogen bonded to the backbone amide of residue-50 and to the Asp-15 carboxylate, and it is approximately 4 A from the closest sulfur atom of the cluster. Despite the water molecule linking the cluster more directly to the solvent, proton transfer is not accelerated. A detailed analysis reveals that Asp-15 remains a central part of the mechanism. However, the electrostatic coupling between cluster and carboxylate is almost completely quenched, so that cluster reduction no longer induces such a favorable shift in the carboxylate pK, and protonation of the base no longer induces a significant shift in the pK of the cluster. The electrostatic coupling is crucial for maintaining the efficiency of proton transfer both to and from the cluster, over a range of pH values.

Organizational Affiliation

Department of Chemistry, Oxford University, South Parks Road, Oxford, OX1 3QR, England.

Macromolecule Content

Total Structure Weight: 12.8 kDa
Atom Count: 944
Modeled Residue Count: 106
Deposited Residue Count: 107
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin I	A	107	Azotobacter vinelandii	Mutation(s): 1
UniProt
Find proteins for P00214 (Azotobacter vinelandii) Explore P00214 Go to UniProtKB: P00214
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00214
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain C [auth A]