[English] 日本語
Yorodumi
- PDB-6zzn: Crystal structure of the cubic catalytic core of the Mycobacteriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zzn
TitleCrystal structure of the cubic catalytic core of the Mycobacterium tuberculosis branched-chain alphaketoacid acyltransferase component (E2b).
ComponentsDihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex
KeywordsTRANSFERASE / BCKDH / acyltransferase / lipoamide / mycobacterium / tuberculosis / CoA
Function / homology
Function and homology information


dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity / lipoic acid binding / acetyltransferase activity / peptidoglycan-based cell wall / plasma membrane / cytoplasm
Similarity search - Function
Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVilela, P. / Bellinzoni, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-JSV8-0003 France
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex.
Authors: Eduardo M Bruch / Pierre Vilela / Lu Yang / Alexandra Boyko / Norik Lexa-Sapart / Bertrand Raynal / Pedro M Alzari / Marco Bellinzoni /
Abstract: α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, ...α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high-molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.
History
DepositionAug 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 15, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8924
Polymers24,7041
Non-polymers1873
Water6,071337
1
A: Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)597,40096
Polymers592,90724
Non-polymers4,49272
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area99950 Å2
ΔGint-419 kcal/mol
Surface area191390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.073, 214.073, 214.073
Angle α, β, γ (deg.)90, 90, 90
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21A-760-

HOH

31A-790-

HOH

41A-835-

HOH

-
Components

#1: Protein Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex / Branched-chain alpha-ketoacid dehydrogenase complex component E2 / BCKADH E2 / Dihydrolipoyllysine- ...Branched-chain alpha-ketoacid dehydrogenase complex component E2 / BCKADH E2 / Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase


Mass: 24704.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: bkdC, pdhC, Rv2495c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O06159, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M imidazole pH 6.5, 4 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.5→49.112 Å / Num. obs: 67274 / % possible obs: 100 % / Redundancy: 17.2 % / CC1/2: 0.999 / Rpim(I) all: 0.023 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.526 Å / Num. unique obs: 3308 / CC1/2: 0.748 / Rpim(I) all: 0.391

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L60

3l60


Resolution: 1.5→49.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.058 / SU Rfree Blow DPI: 0.055 / SU Rfree Cruickshank DPI: 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 3413 -RANDOM
Rwork0.1897 ---
obs0.1899 67274 100 %-
Displacement parametersBiso mean: 28.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.5→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 13 337 2018
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081730HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932360HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d586SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it1730HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion238SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1945SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion13.45
LS refinement shellResolution: 1.5→1.51 Å
RfactorNum. reflection% reflection
Rfree0.1907 70 -
Rwork0.1935 --
obs0.1933 1346 100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
111.7379-14.5526.758523.3373-9.39716.4380.06020.2307-0.54890.2307-1.29581.2415-0.54891.24151.23560.0694-0.1202-0.10010.27120.10710.22353.466233.634636.7873
20.59370.1231-0.08990.64280.02260.75750.0271-0.0248-0.0533-0.0248-0.00530.103-0.05330.103-0.0218-0.054-0.0195-0.0063-0.0386-0.0092-0.047741.072735.380916.2785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|166 - A|188 }
2X-RAY DIFFRACTION2{ A|189 - A|393 }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more