3HST

N-Terminal RNASE H domain of rv2228c from mycobacterium tuberculosis as a fusion protein with maltose binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.

Watkins, H.A.Baker, E.N.

(2010) J Bacteriol 192: 2878-2886

  • DOI: 10.1128/JB.01615-09
  • Primary Citation of Related Structures:  
    3HST

  • PubMed Abstract: 
  • The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase (CobC) ...

    The open reading frame Rv2228c from Mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. The N-terminal domain is homologous with prokaryotic and eukaryotic RNase H domains and the C-terminal domain with alpha-ribazole phosphatase (CobC). The N-terminal domain of Rv2228c (Rv2228c/N) and the full-length protein were expressed as fusions with maltose binding protein (MBP). Rv2228c/N was shown to have RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein was shown to have additional CobC activity. The crystal structure of the MBP-Rv2228c/N fusion protein was solved by molecular replacement and refined at 2.25-A resolution (R = 0.182; R(free) = 0.238). The protein is monomeric in solution but associates in the crystal to form a dimer. The Rv2228c/N domain has the classic RNase H fold and catalytic machinery but lacks several surface features that play important roles in the cleavage of RNA/DNA hybrids by other RNases H. The absence of either the basic protrusion of some RNases H or the hybrid binding domain of others appears to be compensated by the C-terminal CobC domain in full-length Rv2228c. The double-stranded-RNase activity of Rv2228c/N contrasts with classical RNases H and is attributed to the absence in Rv2228c/N of a key phosphate binding pocket.


    Organizational Affiliation

    Maurice Wilkins Centre for Molecular Biodiscovery and School of Biological Sciences, 3A Symonds Street, Private Bag 92019, Auckland, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic proteinA, C387Escherichia coli K-12Mutation(s): 0 
Gene Names: b4034JW3994malEMaltose Binding Protein
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Rv2228c/MT2287B, D141Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT2287MTCY427.09cRv2228c
EC: 3 (PDB Primary Data), 3.1.26.4 (UniProt), 3.1.3.73 (UniProt)
Find proteins for P9WLH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WLH5 
Go to UniProtKB:  P9WLH5
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseE, F3 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR

Download Ideal Coordinates CCD File 
I [auth C]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A], H [auth C], J [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900009
Query on PRD_900009
E, Falpha-maltotrioseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.632α = 90
b = 101.383β = 109.01
c = 76.091γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PHENIXrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary