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- PDB-7ruv: Structure of Human ATP:Cobalamin Adenosyltransferase E193K bound ... -

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Basic information

Entry
Database: PDB / ID: 7ruv
TitleStructure of Human ATP:Cobalamin Adenosyltransferase E193K bound to adenosylcobalamin
ComponentsCorrinoid adenosyltransferase
KeywordsTRANSFERASE / ATP:cobalamin adenosyl transferase / cobalamin / vitamin B12 / patient mutation
Function / homology
Function and homology information


Defective MMAB causes MMA, cblB type / cobalamin metabolic process / Cobalamin (Cbl) metabolism / corrinoid adenosyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cobalamin binding / transferase activity, transferring alkyl or aryl (other than methyl) groups / mitochondrial matrix / ATP binding
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / : / Corrinoid adenosyltransferase MMAB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMascarenhas, R. / Gouda, H. / Koutmos, M. / Banerjee, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK45776 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions.
Authors: Gouda, H. / Mascarenhas, R. / Pillay, S. / Ruetz, M. / Koutmos, M. / Banerjee, R.
History
DepositionAug 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38916
Polymers86,8834
Non-polymers6,50612
Water2,036113
1
A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,09715
Polymers65,1623
Non-polymers4,93512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10180 Å2
ΔGint-32 kcal/mol
Surface area19880 Å2
MethodPISA
2
B: Corrinoid adenosyltransferase
D: Corrinoid adenosyltransferase
hetero molecules

C: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,02311
Polymers65,1623
Non-polymers4,8618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_544-x+y+1/3,-x-1/3,z-1/31
Buried area9440 Å2
ΔGint-36 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.181, 121.181, 169.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-301-

K

21A-302-

MG

31A-436-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Corrinoid adenosyltransferase / Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / ...Cob(II)alamin adenosyltransferase / Cob(II)yrinic acid a / c-diamide adenosyltransferase / Cobinamide/cobalamin adenosyltransferase / Methylmalonic aciduria type B protein


Mass: 21720.760 Da / Num. of mol.: 4 / Mutation: E193K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMAB / Production host: Escherichia coli (E. coli) / References: UniProt: Q96EY8, corrinoid adenosyltransferase

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Non-polymers , 6 types, 125 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM HEPES pH 7.5, 150 mM KCl, 2 mM MgCl2, 2 mM TCEP and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→33 Å / Num. obs: 52113 / % possible obs: 96 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.0118 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 3363 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IDX

2idx


Resolution: 2.1→32.999 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 2625 5.04 %
Rwork0.1848 49438 -
obs0.1865 52063 95.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.77 Å2 / Biso mean: 48.7034 Å2 / Biso min: 28.62 Å2
Refinement stepCycle: final / Resolution: 2.1→32.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 445 113 5180
Biso mean--45.15 47.02 -
Num. residues----599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13820.33921070.2981198274
2.1382-2.17930.3121300.2755218181
2.1793-2.22380.2965940.2522238087
2.2238-2.27220.29721130.2276248891
2.2722-2.3250.25751290.2136262695
2.325-2.38310.26931620.2217262398
2.3831-2.44750.26621210.21182722100
2.4475-2.51950.25191740.19992677100
2.5195-2.60080.24581280.19582711100
2.6008-2.69380.22921620.19832723100
2.6938-2.80160.25181450.20082684100
2.8016-2.9290.26151420.20262718100
2.929-3.08330.21761410.20052721100
3.0833-3.27630.26381410.19722700100
3.2763-3.5290.24841350.1855269599
3.529-3.88370.2141660.18112700100
3.8837-4.44450.17111440.15462708100
4.4445-5.59510.19731360.16622715100
5.5951-32.90.16361550.1603268499

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