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- PDB-2zqq: Crystal structure of human AUH (3-methylglutaconyl-coa hydratase)... -

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Basic information

Entry
Database: PDB / ID: 2zqq
TitleCrystal structure of human AUH (3-methylglutaconyl-coa hydratase) mixed with (AUUU)24A RNA
ComponentsMethylglutaconyl-CoA hydratase
KeywordsLYASE / BETA SPIRAL / Branched-chain amino acid catabolism / Disease mutation / Mitochondrion / RNA-binding / Transit peptide / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


methylglutaconyl-CoA hydratase / itaconyl-CoA hydratase / methylglutaconyl-CoA hydratase activity / itaconyl-CoA hydratase activity / 3-methylglutaconic aciduria / L-leucine catabolic process / enoyl-CoA hydratase activity / Branched-chain amino acid catabolism / fatty acid beta-oxidation / mRNA 3'-UTR binding ...methylglutaconyl-CoA hydratase / itaconyl-CoA hydratase / methylglutaconyl-CoA hydratase activity / itaconyl-CoA hydratase activity / 3-methylglutaconic aciduria / L-leucine catabolic process / enoyl-CoA hydratase activity / Branched-chain amino acid catabolism / fatty acid beta-oxidation / mRNA 3'-UTR binding / mitochondrial matrix / mitochondrion
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methylglutaconyl-CoA hydratase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKurimoto, K. / Kuwasako, K. / Muto, Y. / Nureki, O. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2009
Title: AU-rich RNA-binding induces changes in the quaternary structure of AUH
Authors: Kurimoto, K. / Kuwasako, K. / Sandercock, A.M. / Unzai, S. / Robinson, C.V. / Muto, Y. / Yokoyama, S.
History
DepositionAug 16, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylglutaconyl-CoA hydratase
B: Methylglutaconyl-CoA hydratase
C: Methylglutaconyl-CoA hydratase
D: Methylglutaconyl-CoA hydratase
E: Methylglutaconyl-CoA hydratase
F: Methylglutaconyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)175,4296
Polymers175,4296
Non-polymers00
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22280 Å2
ΔGint-171 kcal/mol
Surface area60640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.740, 129.276, 88.586
Angle α, β, γ (deg.)90.00, 94.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methylglutaconyl-CoA hydratase / AU-specific RNA-binding enoyl-CoA hydratase / AU-binding protein/enoyl-CoA hydratase


Mass: 29238.154 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AUH / Plasmid: PGEX6P1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13825, methylglutaconyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: DROP: 50MM HEPES, 1.0M AMMONIUM SULFATE, 1.0% PEG400, RESERVOIR: 100MM HEPES, 2.0M AMMONIUM SULFATE, 2.0% PEG400, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorDetector: CCD / Date: May 23, 2002
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 88656 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 2.29 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 23.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.725 / Rsym value: 0.156 / % possible all: 85.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HZD

1hzd


Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.246 --RANDOM
Rwork0.205 ---
obs0.205 88656 92.8 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11912 0 0 508 12420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.42
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.28 Å /
RfactorNum. reflection
Rfree0.2956 814
Rwork0.2445 -

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