9M1Q | pdb_00009m1q

Crystal structure of N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.265 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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Literature

Structural insight into an intertwined homodimer of the N-terminal domain of hypothetical protein Rv1421 from Mycobacterium tuberculosis H37Rv.

Park, J.Lee, K.S.

(2025) Biochem Biophys Res Commun 779: 152447-152447

  • DOI: https://doi.org/10.1016/j.bbrc.2025.152447
  • Primary Citation of Related Structures:  
    9M1Q

  • PubMed Abstract: 

    Mycobacterium tuberculosis Rv1421 (MtRv1421) is a hypothetical protein that may participate in the nucleotide-sugar metabolism for cell wall homeostasis. Our previous studies have suggested that MtRv1421 may be involved in the regulatory device mediated by uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), a precursor in peptidoglycan synthesis. However, the detailed molecular functions of MtRv1421 are unclear due to a lack of structural information. To elucidate its functional domain structure, we have constructed the truncated MtRv1421 containing the N-terminal domain (MtRv1421-NTD) and determined its crystal structure at a resolution of 1.7 Å. The overall structure of MtRv1421-NTD showed an intertwined homodimer in which the β5 strand and α6 helix of one subunit were exchanged with those of the other. In addition, the crystal structure of MtRv1421-NTD contained an atypical kinase fold caused by an open conformation of the hinge region between the α4 and α5 helices of each subunit. Our results provide structural insights into the molecular understanding of MtRv1421, including interactions between its functional domains and the binding of UDP-GlcNAc to the putative ligand-binding pocket of MtRv1421-NTD.


  • Organizational Affiliation
    • Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, 46252, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleotide-binding protein Rv1421
A, B
174Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv1421MTCY21B4.39
UniProt
Find proteins for P9WFQ3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFQ3 
Go to UniProtKB:  P9WFQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFQ3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G (Subject of Investigation/LOI)
Query on P6G

Download Ideal Coordinates CCD File 
C [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.008α = 90
b = 58.547β = 133.116
c = 84.87γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2021R1F1A1047349

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references