3HSS | pdb_00003hss

A higher resolution structure of Rv0554 from Mycobacterium tuberculosis complexed with malonic acid

PDB DOI: https://doi.org/10.2210/pdb3HSS/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-10 Released: 2010-05-26
Deposition Author(s): Johnston, J.M., Baker, E.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.219 (Depositor), 0.212 (DCC)
R-Value Work:
0.193 (Depositor), 0.184 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis.

Johnston, J.M., Jiang, M., Guo, Z., Baker, E.N.

(2010) Acta Crystallogr D Biol Crystallogr 66: 909-917

PubMed: 20693690 Search on PubMed
DOI: https://doi.org/10.1107/S0907444910025771
Primary Citation Related Structures:
3E3A, 3HSS, 3HYS

PubMed Abstract:
Mycobacterium tuberculosis, the cause of tuberculosis, is a devastating human pathogen against which new drugs are urgently needed. Enzymes from the biosynthetic pathway for menaquinone are considered to be valid drug targets. The protein encoded by the open reading frame Rv0554 has been expressed, purified and subjected to structural and functional analysis to test for a putative role in menaquinone biosynthesis. The crystal structure of Rv0554 has been solved and refined in two different space groups at 2.35 and 1.9 A resolution. The protein is dimeric, with an alpha/beta-hydrolase monomer fold. In each monomer, a large cavity adjacent to the catalytic triad is enclosed by a helical lid. Dimerization is mediated by the lid regions. Small-molecule additives used in crystallization bind in the active site, but no binding of ligands related to menaquinone biosynthesis could be detected and functional assays failed to support possible roles in menaquinone biosynthesis.

Organizational Affiliation

School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand.

Macromolecule Content

Total Structure Weight: 65.42 kDa
Atom Count: 4,705
Modeled Residue Count: 535
Deposited Residue Count: 586
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative Bromoperoxidase	A, B	293	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: bpoC, MT0580, Rv0554 EC: 1.11.1
UniProt
Find proteins for P9WNH1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNH1 Go to UniProtKB: P9WNH1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WNH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B], O [auth B]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain O [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] F [auth A] G [auth A] H [auth A] K [auth A] D [auth A], F [auth A], G [auth A], H [auth A], K [auth A], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.219 (Depositor), 0.212 (DCC)
R-Value Work: 0.193 (Depositor), 0.184 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.454	α = 90
b = 100.454	β = 90
c = 135.162	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Johnston, J.M.

Baker, E.N.

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2015-04-29
Changes: Non-polymer description
Version 1.3: 2017-11-01
Changes: Advisory, Refinement description
Version 1.4: 2024-02-21
Changes: Advisory, Data collection, Database references, Derived calculations