9NZY | pdb_00009nzy

Structure of Methanogen MtxX (Methanogen Marker Protein MMP4) from Methanothermobacter thermautotrophicus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.185 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.163 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9NZY

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

Literature

Crystal structure of methanogen MtxX (Methanogen Marker Protein MMP4) from Methanothermobacter thermautotrophicus Delta H.

Sutherland-Smith, A.J., Carbone, V., Kaziur-Cegla, W., Woermann, M., Schofield, L.R., Ronimus, R.S.

(2026) FEMS Microbes 7: xtag011-xtag011

  • DOI: https://doi.org/10.1093/femsmc/xtag011
  • Primary Citation Related Structures: 
    9NZY

  • PubMed Abstract: 

    MtxX, also known as Methanogen Marker Protein 4 (MMP4), is a member of the group of proteins conserved in archaeal methanogens called the Methanogen Marker Proteins (MMPs). Owing to this taxonomic distribution the MMPs are presumed to have roles related to methanogenesis or are evidence for an evolutionary history associated with methanogenic processes. MtxX is sequence-annotated as either a methyltransferase (EC 2.1.1.-) or a phosphate acetyl/butyryltransferase (EC 2.3.1.8/2.3.1.19). Gene synteny analysis shows mtxX is located next to other MMP genes in Methanomicrobiales, Methanotrichales, and Methanocaldococcus genomes, while in Methanobacteria and Methanococci it is positioned adjacent to undecaprenyl pyrophosphate synthase, a cell wall biosynthesis enzyme. We describe the crystal structure for MtxX from Methanothermobacter thermautotrophicus ΔH showing that it has a protein fold homologous to phosphate acetyltransferases and decarboxylating NAD(P)-dependent dehydrogenases. The MtxX structure has a conserved binding cleft which is the presumptive functional site based on crystallographic symmetry-related molecular binding interactions and structural homology.

    • Organizational Affiliation: 
    • School of Food Technology and Natural Sciences, Massey University, Palmerston North 4442, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 60.45 kDa 
  • Atom Count: 3,882 
  • Modeled Residue Count: 464 
  • Deposited Residue Count: 550 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized methyltransferase MTH_231
A, B
275Methanothermobacter thermautotrophicus str. Delta HMutation(s): 0 
Gene Names: MTH_231
EC: 2.1.1
UniProt
Find proteins for O26333 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26333 
Go to UniProtKB:  O26333
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26333
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO


Download:Ideal Coordinates CCD File
C [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.185 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.163 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.484α = 90
b = 72.31β = 96.115
c = 65.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentNew Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references