6KBW | pdb_00006kbw

Crystal structure of Tmm from Myroides profundi D25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.206 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Oxidation of trimethylamine to trimethylamine N-oxide facilitates high hydrostatic pressure tolerance in a generalist bacterial lineage.

Qin, Q.L.Wang, Z.B.Su, H.N.Chen, X.L.Miao, J.Wang, X.J.Li, C.Y.Zhang, X.Y.Li, P.Y.Wang, M.Fang, J.Lidbury, I.Zhang, W.Zhang, X.H.Yang, G.P.Chen, Y.Zhang, Y.Z.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf9941
  • Primary Citation Related Structures: 
    6KBW

  • PubMed Abstract: 

    High hydrostatic pressure (HHP) is a characteristic environmental factor of the deep ocean. However, it remains unclear how piezotolerant bacteria adapt to HHP. Here, we identify a two-step metabolic pathway to cope with HHP stress in a piezotolerant bacterium. Myroides profundi D25 T , obtained from a deep-sea sediment, can take up trimethylamine (TMA) through a previously unidentified TMA transporter, TmaT, and oxidize intracellular TMA into trimethylamine N -oxide (TMAO) by a TMA monooxygenase, Mp Tmm. The produced TMAO is accumulated in the cell, functioning as a piezolyte, improving both growth and survival at HHP. The function of the TmaT- Mp Tmm pathway was further confirmed by introducing it into Escherichia coli and Bacillus subtilis Encoded TmaT-like and Mp Tmm-like sequences extensively exist in marine metagenomes, and other marine Bacteroidetes bacteria containing genes encoding TmaT-like and Mp Tmm-like proteins also have improved HHP tolerance in the presence of TMA, implying the universality of this HHP tolerance strategy in marine Bacteroidetes.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.

Macromolecule Content 

  • Total Structure Weight: 112.92 kDa 
  • Atom Count: 8,422 
  • Modeled Residue Count: 892 
  • Deposited Residue Count: 934 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trimethylamine monooxygenase
A, B
467Myroides profundiMutation(s): 0 
Gene Names: MPR_3295
EC: 1.14.13.148
UniProt
Find proteins for A0A0B5RNJ4 (Myroides profundi)
Explore A0A0B5RNJ4 
Go to UniProtKB:  A0A0B5RNJ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B5RNJ4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.206 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.543α = 90
b = 99.372β = 90
c = 144.925γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description