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- PDB-2ybo: The x-ray structure of the SAM-dependent uroporphyrinogen III met... -

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Basic information

Entry
Database: PDB / ID: 2ybo
TitleThe x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH
ComponentsMETHYLTRANSFERASE
KeywordsTRANSFERASE / SUMT / NIRE / HEME D1 BIOSYNTHESIS
Function / homology
Function and homology information


uroporphyrinogen-III C-methyltransferase / uroporphyrin-III C-methyltransferase activity / siroheme biosynthetic process / cobalamin biosynthetic process / methylation
Similarity search - Function
Uroporphyrin-III C-methyltransferase / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase ...Uroporphyrin-III C-methyltransferase / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / uroporphyrinogen-III C-methyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStorbeck, S. / Saha, S. / Krausze, J. / Klink, B.U. / Heinz, D.W. / Layer, G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen ...Title: Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen III Methyltransferases.
Authors: Storbeck, S. / Saha, S. / Krausze, J. / Klink, B.U. / Heinz, D.W. / Layer, G.
History
DepositionMar 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7862
Polymers31,4021
Non-polymers3841
Water3,513195
1
A: METHYLTRANSFERASE
hetero molecules

A: METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5734
Polymers62,8042
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5230 Å2
ΔGint-27.4 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.900, 115.100, 76.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein METHYLTRANSFERASE / / PROBABLE UROPORPHYRIN-III C-METHYLTRANSFERASE / UROPORPHYRINOGEN III METHYLTRANFERASE


Mass: 31402.012 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET32A_PRES2-4_NIRE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P95417, uroporphyrinogen-III C-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN WAS CRYSTALLIZED FROM 24% PEG 6000, 0.1 M TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Oct 22, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.31 Å / Num. obs: 19360 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.19
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.58 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S4D

1s4d


Resolution: 2→26.915 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.853 / SU B: 12.098 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.231 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 915 5.02 %RANDOM
Rwork0.2349 ---
obs0.238 18294 98.281 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 14.459 Å2
Baniso -1Baniso -2Baniso -3
1-0.638 Å20 Å20 Å2
2---0.37 Å20 Å2
3----0.268 Å2
Refinement stepCycle: LAST / Resolution: 2→26.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 26 195 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221923
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9992618
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5875246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24823.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53215302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3131518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2997
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21303
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.299
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.51232
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2121960
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6643691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6934.5658
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 65 -
Rwork0.291 1236 -
obs--97.09 %
Refinement TLS params.

Method: refined / 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)
13.1229-0.9568-0.50811.52230.78711.8652-0.0585-0.10650.01290.1322-0.03980.0447-0.0121-0.0990.09830.01780.0040.00210.045-0.0170.018816.280930.940424.3623
20.72190.22570.10672.1078-0.47291.93190.0219-0.01320.06250.0135-0.07010.0127-0.0030.00920.04820.0270.006-0.00390.03440.010.02935.754112.053430.7636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 135
2X-RAY DIFFRACTION2A136 - 266

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