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- PDB-2hdh: BIOCHEMICAL CHARACTERIZATION AND STRUCTURE DETERMINATION OF HUMAN... -

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Basic information

Entry
Database: PDB / ID: 2hdh
TitleBIOCHEMICAL CHARACTERIZATION AND STRUCTURE DETERMINATION OF HUMAN HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE PROVIDE INSIGHT INTO CATALYTIC MECHANISM
ComponentsL-3-HYDROXYACYL COA DEHYDROGENASE
KeywordsOXIDOREDUCTASE / BETA OXIDATION / SCHAD / CATALYTIC ACTIVITY: L-3-HYDROXYACYL-COA + NAD(+) = 3-OXOACYL-COA + NADH
Function / homology
Function and homology information


Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / fatty acid beta-oxidation / NAD+ binding / Mitochondrial protein degradation ...Beta oxidation of butanoyl-CoA to acetyl-CoA / Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA / Beta oxidation of hexanoyl-CoA to butanoyl-CoA / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / 3-hydroxyacyl-CoA dehydrogenase / (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / fatty acid beta-oxidation / NAD+ binding / Mitochondrial protein degradation / regulation of insulin secretion / response to activity / negative regulation of insulin secretion / response to insulin / transferase activity / positive regulation of cold-induced thermogenesis / spermatogenesis / cell differentiation / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / nucleoplasm / identical protein binding / cytoplasm
Similarity search - Function
: / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 ...: / 3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBarycki, J.J. / Bratt, J.M. / Banaszak, L.J.
Citation
Journal: Biochemistry / Year: 1999
Title: Biochemical characterization and crystal structure determination of human heart short chain L-3-hydroxyacyl-CoA dehydrogenase provide insights into catalytic mechanism.
Authors: Barycki, J.J. / O'Brien, L.K. / Bratt, J.M. / Zhang, R. / Sanishvili, R. / Strauss, A.W. / Banaszak, L.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: Structure of L-3-Hydroxyacyl-Coenzyme a Dehydrogenase: Preliminary Chain Tracing at 2.8-A Resolution
Authors: Birktoff, J.J. / Holden, H.M. / Hamlin, R. / Xuong, N.H. / Banaszak, L.J.
History
DepositionDec 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 12, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-3-HYDROXYACYL COA DEHYDROGENASE
B: L-3-HYDROXYACYL COA DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9774
Polymers64,6502
Non-polymers1,3272
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-44 kcal/mol
Surface area25480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.650, 86.500, 169.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein L-3-HYDROXYACYL COA DEHYDROGENASE / E.C.1.1.1.35 / SCHAD


Mass: 32325.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: EXPRESSED AS SELENOMETHIONINE-SUBSTITUTED PROTEIN. PROTEIN WAS EXPRESSED WITH A C-TERMINAL HEXAMERIC HISTIDINE TAG.
Organ: HEART / Organelle: MITOCHONDRIAL / Production host: Escherichia coli (E. coli)
References: UniProt: Q16836, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE TO BE PUBLISHED BY O'BRIEN,SIMS,GIBSON,& STRAUSS

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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: 2.7 Å3/Da / Density % sol: 57.07 %
Description: STATISTICS ARE FOR 1.0781 ANGSTROM DATA SET WITH BIJVOETS MERGED.
Crystal growpH: 6.5 / Details: 0.1 M ADA, PH 6.5, 15-20% PEG 4000
Components of the solutions
IDConc.NameCrystal-IDSol-ID
10.1 M ADA11
215-20% PEG 400011
315-20% PEG 400012
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
25 mMNAD+1drop
350 mMN-[2-acetamido]-2-iminodiacetic acid1reservoir
414-19 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0781, 0.9794, 0.9792, 0.9355
DetectorType: APS-1 / Detector: CCD / Date: Feb 15, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07811
20.97941
30.97921
40.93551
ReflectionResolution: 2.2→20 Å / Num. obs: 34779 / % possible obs: 90.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 40.7 Å2 / Rsym value: 3.5 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.28 Å / % possible all: 60.3
Reflection
*PLUS
Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 60.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS0.3refinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 375652.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. ELECTRON DENSITY WAS NOT OBSERVED FOR THE FIRST ELEVEN AMINO ACIDS OF EACH SUBUNIT AND THE MAJORITY OF THE C-TERMINAL HEXAMERIC HISTIDINE TAG.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1613 5 %RANDOM
Rwork0.198 ---
all-32575 --
obs-32575 84.4 %-
Displacement parametersBiso mean: 40.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-6 Å
Luzzati sigma a0.43 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4483 0 88 253 4824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.281.5
X-RAY DIFFRACTIONx_mcangle_it4.872
X-RAY DIFFRACTIONx_scbond_it5.642
X-RAY DIFFRACTIONx_scangle_it8.022.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 145 4.5 %
Rwork0.316 3108 -
obs--51.5 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it3.281.5
X-RAY DIFFRACTIONc_scbond_it5.642
X-RAY DIFFRACTIONc_mcangle_it4.872
X-RAY DIFFRACTIONc_scangle_it8.022.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.365 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.316

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