1HRK | pdb_00001hrk

CRYSTAL STRUCTURE OF HUMAN FERROCHELATASE

PDB DOI: https://doi.org/10.2210/pdb1HRK/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes OPM

Deposited: 2000-12-21 Released: 2001-06-22
Deposition Author(s): Wu, C.K., Dailey, H.A., Rose, J.P., Burden, A., Sellers, V.M., Wang, B.-C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.226 (Depositor)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.

Wu, C.K., Dailey, H.A., Rose, J.P., Burden, A., Sellers, V.M., Wang, B.C.

(2001) Nat Struct Biol 8: 156-160

PubMed: 11175906 Search on PubMed
DOI: https://doi.org/10.1038/84152
Primary Citation Related Structures:
1HRK

PubMed Abstract:
Human ferrochelatase (E.C. 4.99.1.1) is a homodimeric (86 kDa) mitochondrial membrane-associated enzyme that catalyzes the insertion of ferrous iron into protoporphyrin to form heme. We have determined the 2.0 A structure from the single wavelength iron anomalous scattering signal. The enzyme contains two NO-sensitive and uniquely coordinated [2Fe-2S] clusters. Its membrane association is mediated in part by a 12-residue hydrophobic lip that also forms the entrance to the active site pocket. The positioning of highly conserved residues in the active site in conjunction with previous biochemical studies support a catalytic model that may have significance in explaining the enzymatic defects that lead to the human inherited disease erythropoietic protoporphyria.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602-7229, USA.

Macromolecule Content

Total Structure Weight: 85.07 kDa
Atom Count: 6,486
Modeled Residue Count: 718
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERROCHELATASE	A, B	359	Homo sapiens	Mutation(s): 2 EC: 4.99.1.1 (PDB Primary Data), 4.98.1.1 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P22830 (Homo sapiens) Explore P22830 Go to UniProtKB: P22830
PHAROS: P22830 GTEx: ENSG00000066926
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22830
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHD Query on CHD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]