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

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Basic information

Entry
Database: PDB / ID: 2ybq
TitleThe x-ray structure of the SAM-dependent uroporphyrinogen III methyltransferase NirE from Pseudomonas aeruginosa in complex with SAH and uroporphyrinogen III
ComponentsMETHYLTRANSFERASE
KeywordsTRANSFERASE / 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 / uroporphyrinogen-III C-methyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 9, 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)32,3893
Polymers31,1681
Non-polymers1,2212
Water2,324129
1
A: METHYLTRANSFERASE
hetero molecules

A: METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7786
Polymers62,3352
Non-polymers2,4424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5600 Å2
ΔGint-26.4 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.853, 116.702, 76.988
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 / UROPORPHYRINOGEN III METHYLTRANFERASE


Mass: 31167.736 Da / Num. of mol.: 1
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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-UP2 / UROPORPHYRINOGEN III


Mass: 836.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H44N4O16
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.44 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 1.26 M AMMONIUM SULFATE, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2010
RadiationMonochromator: SI(100) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 18362 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YBO

2ybo


Resolution: 2→32.13 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.846 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25904 919 5 %RANDOM
Rwork0.22626 ---
obs0.22795 17443 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.641 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--1.17 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2→32.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 86 129 2032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0272652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.245239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98122.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19115298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2731519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2868
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21277
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5631.51201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02521911
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6063746
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7214.5741
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
Rfree0.34 71 -
Rwork0.222 1341 -
obs--100 %
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)
16.19121.54860.42570.65410.33431.25340.02650.01320.5447-0.0211-0.16440.0844-0.23710.13490.13790.1287-0.03320.01790.17340.08060.245510.155235.599616.2873
28.13380.1930.89835.0714-1.6555.37440.08630.8662-0.0612-0.76440.020.5051-0.2344-0.3788-0.10630.2755-0.0579-0.03860.42640.08850.219912.094533.23615.715
31.2431.13270.64881.87220.08191.18680.05360.1815-0.1446-0.0359-0.0766-0.28030.14370.26420.0230.04550.02640.02670.12860.0210.066110.256520.962414.7548
40.549-0.44010.23131.02110.66551.41780.02280.0176-0.0026-0.1035-0.05190.05150.0682-0.09060.02920.14870.0013-0.01940.0801-0.00690.0461-5.800810.54445.2337
56.3324-4.1138-0.851213.066616.915325.89370.22941.29010.0014-1.1066-0.2630.0739-1.35470.910.03360.59090.1485-0.08350.53540.08070.4499-17.33426.70329.0634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 49
2X-RAY DIFFRACTION2A50 - 82
3X-RAY DIFFRACTION3A83 - 171
4X-RAY DIFFRACTION4A172 - 255
5X-RAY DIFFRACTION5A256 - 265

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