9CRZ | pdb_00009crz

Acanthamoeba Polyphaga Mimivirus R655

PDB DOI: https://doi.org/10.2210/pdb9CRZ/pdb

Classification: VIRAL PROTEIN
Organism(s): Acanthamoeba polyphaga mimivirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-23 Released: 2025-08-06
Deposition Author(s): Morin, K.H., Buhlheller, C., Kim, J.S., Richards, S.J., Guo, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.252 (Depositor), 0.244 (DCC)
R-Value Work:
0.210 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The Crystal Structure of Acanthamoeba Polyphaga Mimivirus R655 and Its Potential Glycosaminoglycan Glycosyltransferase Activity.

Kim, J.S., Zhang, B., Morin, K.H., Gilliam, M., Guo, H.

(2025) Biochemistry 64: 2737-2744

PubMed: 40545624 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.biochem.5c00058
Primary Citation Related Structures:
9CRZ

PubMed Abstract:
Acanthamoeba polyphaga mimivirus (APMV) is a giant virus that encodes over 1,000 genes, many of which are involved in protein post-translational modifications, such as glycosylation. Here, we present the high-resolution crystal structure of a putative mimiviral glycosyltransferase R655 (Uniprot accession ID: Q5UQ62). R655 consists of a Rossmann domain with a glycosyltransferase family A (GT-A) fold followed by a CPW-WPC domain, connected by a long loop. The N-terminal region of this loop crosses over the Mn ²⁺ and uridine diphosphate (UDP) binding pocket in the Rossmann domain, suggesting that it may function as a pocket cap. Within the binding pocket, the aspartate residue in the EXD motif coordinates Mn ²⁺ while the glutamate residue is positioned to interact with the sugar moiety of the UDP-sugar. UDP is sandwiched between Leu11 and an α helix, the diphosphate of which is stabilized by a nearby Arg17. R655 contains two strips of electropositive surfaces near the Mn ²⁺/UDP binding site, suggesting that it may recognize negatively charged substrates. Structural comparisons of R655 with homologous proteins in the AlphaFold Protein Structure Database and the Worldwide Protein Data Bank identified top matches, including collagen galactosyltransferases and the Vaccinia virus H3 envelope protein, a heparan sulfate-binding glycosyltransferase. However, enzymatic activity assays revealed that R655 exhibits activity toward negatively charged glycosaminoglycans (GAGs) rather than collagen, consistent with the structural findings. Kinetic parameters, cofactor, and sugar donor preferences were characterized. Mutations of the critical residues in the active site and nearby loop abolish R655's enzymatic activity. These results provide novel structural insights into R655 function and suggest a new role of APMV in glycobiology.

Organizational Affiliation

Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, United States.

Macromolecule Content

Total Structure Weight: 80.68 kDa
Atom Count: 5,647
Modeled Residue Count: 624
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glycosyltransferase R655	A, B	346	Acanthamoeba polyphaga mimivirus	Mutation(s): 0 Gene Names: MIMI_R655 EC: 2
UniProt
Find proteins for Q5UQ62 (Acanthamoeba polyphaga mimivirus) Explore Q5UQ62 Go to UniProtKB: Q5UQ62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5UQ62
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.252 (Depositor), 0.244 (DCC)
R-Value Work: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.634	α = 90
b = 96.213	β = 90
c = 133.454	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: 2025-08-06

Deposition Author(s):

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