4H2D

Crystal structure of NDOR1

PDB DOI: 10.2210/pdb4H2D/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-12 Released: 2013-04-17
Deposition Author(s): Banci, L., Bertini, I., Calderone, V., Ciofi-Baffoni, S., Mikolajczyk, M., Jaiswal, D., Winkelmann, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.234
R-Value Work: 0.212
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis.

Banci, L., Bertini, I., Calderone, V., Ciofi-Baffoni, S., Giachetti, A., Jaiswal, D., Mikolajczyk, M., Piccioli, M., Winkelmann, J.

(2013) Proc Natl Acad Sci U S A 110: 7136-7141

PubMed: 23596212 Search on PubMedSearch on PubMed Central
DOI: 10.1073/pnas.1302378110
Primary Citation of Related Structures:
4H2D

PubMed Abstract:

Biogenesis of iron-sulfur cluster proteins is a highly regulated process that requires complex protein machineries. In the cytosolic iron-sulfur protein assembly machinery, two human key proteins--NADPH-dependent diflavin oxidoreductase 1 (Ndor1) and anamorsin--form a stable complex in vivo that was proposed to provide electrons for assembling cytosolic iron-sulfur cluster proteins. The Ndor1-anamorsin interaction was also suggested to be implicated in the regulation of cell survival/death mechanisms. In the present work we unravel the molecular basis of recognition between Ndor1 and anamorsin and of the electron transfer process. This is based on the structural characterization of the two partner proteins, the investigation of the electron transfer process, and the identification of those protein regions involved in complex formation and those involved in electron transfer. We found that an unstructured region of anamorsin is essential for the formation of a specific and stable protein complex with Ndor1, whereas the C-terminal region of anamorsin, containing the [2Fe-2S] redox center, transiently interacts through complementary charged residues with the FMN-binding site region of Ndor1 to perform electron transfer. Our results propose a molecular model of the electron transfer process that is crucial for understanding the functional role of this interaction in human cells.

Related Citations:

NADPH-cytochrome P450 oxidoreductase. Structural basis for hydride and electron transfer.
Hubbard, P.A., Shen, A.L., Paschke, R., Kasper, C.B., Kim, J.J.
(2001) J Biol Chem 276: 29163

Solution structure of the sulfite reductase flavodoxin-like domain from Escherichia coli.
Sibille, N., Blackledge, M., Brutscher, B., Coves, J., Bersch, B.
(2005) Biochemistry 44: 9086

Structure and function of an NADPH-cytochrome P450 oxidoreductase in an open conformation capable of reducing cytochrome P450.
Hamdane, D., Xia, C., Im, S.C., Zhang, H., Kim, J.J., Waskell, L.
(2009) J Biol Chem 284: 11374

Organizational Affiliation:

Magnetic Resonance Center and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Florence, Italy. banci@cerm.unifi.it

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-dependent diflavin oxidoreductase 1	A, B	165	Homo sapiens	Mutation(s): 0 Gene Names: NDOR1, NR1 EC: 1.6 (PDB Primary Data), 1.18.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHB4 (Homo sapiens) Explore Q9UHB4 Go to UniProtKB: Q9UHB4
PHAROS: Q9UHB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHB4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Ligand Interaction