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- PDB-1jl0: Structure of a Human S-Adenosylmethionine Decarboxylase Self-proc... -

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Basic information

Entry
Database: PDB / ID: 1jl0
TitleStructure of a Human S-Adenosylmethionine Decarboxylase Self-processing Ester Intermediate and Mechanism of Putrescine Stimulation of Processing as Revealed by the H243A Mutant
ComponentsS-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME
KeywordsLYASE / SPERMIDINE BIOSYNTHESIS / DECARBOXYLASE / PYRUVATE / S-ADENOSYLMETHIONINE / SANDWICH / ALLOSTERIC ENZYME / PYRUVOYL / ESTER INTERMEDIATE / HYDROXYALANINE
Function / homology
Function and homology information


spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol
Similarity search - Function
S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, conserved site / : / Adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase signature. / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase / S-adenosylmethionine decarboxylase, core / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIAMINOBUTANE / S-adenosylmethionine decarboxylase proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsEkstrom, J.L. / Tolbert, W.D. / Xiong, H. / Pegg, A.E. / Ealick, S.E.
Citation
Journal: Biochemistry / Year: 2001
Title: Structure of a human S-adenosylmethionine decarboxylase self-processing ester intermediate and mechanism of putrescine stimulation of processing as revealed by the H243A mutant.
Authors: Ekstrom, J.L. / Tolbert, W.D. / Xiong, H. / Pegg, A.E. / Ealick, S.E.
#1: Journal: Structure / Year: 1999
Title: The Crystal Structure of Human S-adenosylmethionine Decarboxylase at 2.25 A Resolution Reveals a Novel Fold
Authors: Ekstrom, J.L. / Mathews, I.I. / Stanley, B.A. / Pegg, A.E. / Ealick, S.E.
History
DepositionJul 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 30, 2015Group: Derived calculations
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage ...database_2 / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME
B: S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0176
Polymers76,5972
Non-polymers4214
Water14,520806
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.760, 55.990, 90.210
Angle α, β, γ (deg.)90.00, 109.72, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe enzyme is a dimer and the dimer is in the asymmetric unit.

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Components

#1: Protein S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME / ADOMETDC


Mass: 38298.449 Da / Num. of mol.: 2 / Mutation: H243A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P17707, adenosylmethionine decarboxylase
#2: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, dithiothreitol, tris(hydroxymethyl)aminomethane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %PEG80001reservoir
2100 mMTris-HCl1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03321
DetectorType: SBC-1 / Detector: CCD / Date: Jun 17, 1999
RadiationMonochromator: Sagittally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.5→99 Å / Num. all: 111488 / Num. obs: 111488 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.92 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.6 / Num. unique all: 11200 / % possible all: 99.5
Reflection
*PLUS
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 99.5 %

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JEN

1jen


Resolution: 1.5→19.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 472938.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 10521 10 %RANDOM
Rwork0.215 ---
all0.221 105350 --
obs0.221 105350 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.7209 Å2 / ksol: 0.306614 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20.57 Å2
2--0.1 Å20 Å2
3---0.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 28 806 5855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.432.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 1684 9.9 %
Rwork0.265 15386 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEINMAO.PARAMPROTEINMAO.TOP
X-RAY DIFFRACTION2SS12.PARAMSS12.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.287 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.265

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