9NEV | pdb_00009nev

Acanthamoeba Polyphaga Mimivirus L230

PDB DOI: https://doi.org/10.2210/pdb9NEV/pdb

Classification: VIRAL PROTEIN
Organism(s): Acanthamoeba polyphaga mimivirus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-02-20 Released: 2025-06-04
Deposition Author(s): Chen, T., Buhlheller, C., Guo, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), American Cancer Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.251 (Depositor), 0.251 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of an Fe 2+ -binding-deficient mimiviral collagen lysyl hydroxylase.

Chen, T., Buhlheller, C., Guo, H.

(2025) Acta Crystallogr F Struct Biol Commun 81: 235-240

PubMed: 40314237 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X25003735
Primary Citation Related Structures:
9NEV

PubMed Abstract:
Collagen lysyl hydroxylases catalyze the hydroxylation of collagen lysine residues during collagen synthesis in animals and mimiviruses. Lysyl hydroxylation is crucial for collagen fibrogenesis and function. We previously demonstrated that recombinant mimiviral and human collagen lysyl hydroxylases, isolated from bacterial and mammalian cells, have Fe ²⁺ in their active sites, suggesting that lysyl hydroxylases have a high affinity for Fe ²⁺. We found that Fe ²⁺ binding stabilizes lysyl hydroxylase dimers, although the underlying mechanism remains unclear. Crystal structure analysis of mimiviral lysyl hydroxylase revealed that Fe ²⁺ is coordinated by a 2His-1Asp (His825/His877/Asp827) triad, with a nearby highly conserved histidine residue (His869) involved in an alternative 2His-1Asp triad (His869/His877/Asp827). This unique structural architecture suggests that the alternative 2His-1Asp triad may also bind Fe ²⁺. To investigate whether the alternative 2His-1Asp triad binds Fe ²⁺ and how Fe ²⁺ binding regulates lysyl hydroxylase dimerization, we crystallized the mimiviral lysyl hydroxylase mutant His825Ala, which lacks one 2His-1Asp (His825/His877/Asp827) triad but retains the alternative triad (His869/His877/Asp827). Despite providing Fe ²⁺ during crystallization, we found no electron density near the alternative 2His-1Asp triad in the His825Ala mutant, indicating that the alternative 2His-1Asp triad does not bind Fe ²⁺ with high affinity. Although the His825Ala mutant forms a dimer similar to the wild-type enzyme, conformational changes occur in residues near Ala825, including Leu873, which is critical for dimerization. These structural findings provide new insights into the function and regulation of collagen lysyl hydroxylases.

Organizational Affiliation

Department of Molecular and Cellular Biochemistry, Markey Cancer Center, University of Kentucky, 741 South Limestone Avenue, Lexington, KY 40536-0509, USA.

Macromolecule Content

Total Structure Weight: 54.56 kDa
Atom Count: 3,459
Modeled Residue Count: 395
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Procollagen lysyl hydroxylase and glycosyltransferase	A, B	235	Acanthamoeba polyphaga mimivirus	Mutation(s): 1 Gene Names: MIMI_L230 EC: 1.14.11.4 (PDB Primary Data), 2.4.1 (PDB Primary Data)
UniProt
Find proteins for Q5UQC3 (Acanthamoeba polyphaga mimivirus) Explore Q5UQC3 Go to UniProtKB: Q5UQC3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5UQC3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.251 (Depositor), 0.251 (DCC)
R-Value Work: 0.205 (Depositor), 0.205 (DCC)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.61	α = 90
b = 109.61	β = 90
c = 84.954	γ = 90

Software Package:

Software Name	Purpose
DIALS	data collection
xia2	data reduction
Aimless	data scaling
PHENIX	phasing
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-04

Deposition Author(s):

Chen, T.

Buhlheller, C.

Guo, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R00CA225633
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R37CA278989
American Cancer Society	United States	RSG-24-1156098-01-MM