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- PDB-8gju: Crystal structure of human methylmalonyl-CoA mutase (MMUT) in com... -

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Basic information

Entry
Database: PDB / ID: 8gju
TitleCrystal structure of human methylmalonyl-CoA mutase (MMUT) in complex with methylmalonic acidemia type A protein (MMAA), coenzyme A, and GDP
Components
  • Methylmalonic aciduria type A protein, mitochondrial
  • Methylmalonyl-CoA mutase, mitochondrial
KeywordsIsomerase/Hydrolase / protein-protein complex / isomerase / GTPase / G-protein / cobalamin / vitamin B12 / transport / organometallic cofactor / Isomerase-Hydrolase complex
Function / homology
Function and homology information


Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / Cobalamin (Cbl) metabolism / cobalamin metabolic process / Propionyl-CoA catabolism / sulfur compound metabolic process / Hydrolases; Acting on acid anhydrides ...Defective MMAA causes MMA, cblA type / Defective MUT causes MMAM / propionate metabolic process, methylmalonyl pathway / methylmalonyl-CoA mutase / methylmalonyl-CoA mutase activity / Cobalamin (Cbl) metabolism / cobalamin metabolic process / Propionyl-CoA catabolism / sulfur compound metabolic process / Hydrolases; Acting on acid anhydrides / molecular carrier activity / cobalamin binding / mitochondrial matrix / GTPase activity / GTP binding / protein homodimerization activity / mitochondrion / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl-CoA mutase signature. / Methylmalonyl Co-A mutase-associated GTPase MeaB / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily ...SIMIBI class G3E GTPase, ArgK/MeaB / Methylmalonyl-CoA mutase signature. / Methylmalonyl Co-A mutase-associated GTPase MeaB / Methylmalonyl-CoA mutase, alpha chain, catalytic / Methylmalonyl-CoA mutase, alpha/beta chain, catalytic / Methylmalonyl-CoA mutase / Methylmalonyl-CoA mutase, C-terminal / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
COENZYME A / GUANOSINE-5'-DIPHOSPHATE / Methylmalonyl-CoA mutase, mitochondrial / Methylmalonic aciduria type A protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsMascarenhas, R.M. / Ruetz, M. / Gouda, H. / Yaw, M. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK45776 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99-GM1434820 United States
CitationJournal: Nat Commun / Year: 2023
Title: Architecture of the human G-protein-methylmalonyl-CoA mutase nanoassembly for B 12 delivery and repair.
Authors: Mascarenhas, R. / Ruetz, M. / Gouda, H. / Heitman, N. / Yaw, M. / Banerjee, R.
History
DepositionMar 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Methylmalonic aciduria type A protein, mitochondrial
F: Methylmalonic aciduria type A protein, mitochondrial
J: Methylmalonyl-CoA mutase, mitochondrial
K: Methylmalonyl-CoA mutase, mitochondrial
L: Methylmalonyl-CoA mutase, mitochondrial
A: Methylmalonic aciduria type A protein, mitochondrial
B: Methylmalonic aciduria type A protein, mitochondrial
H: Methylmalonyl-CoA mutase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,85620
Polymers486,9158
Non-polymers4,94012
Water23413
1
D: Methylmalonic aciduria type A protein, mitochondrial
F: Methylmalonic aciduria type A protein, mitochondrial
J: Methylmalonyl-CoA mutase, mitochondrial
K: Methylmalonyl-CoA mutase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,92810
Polymers243,4584
Non-polymers2,4706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16880 Å2
ΔGint-78 kcal/mol
Surface area80700 Å2
MethodPISA
2
L: Methylmalonyl-CoA mutase, mitochondrial
A: Methylmalonic aciduria type A protein, mitochondrial
B: Methylmalonic aciduria type A protein, mitochondrial
H: Methylmalonyl-CoA mutase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,92810
Polymers243,4584
Non-polymers2,4706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17830 Å2
ΔGint-85 kcal/mol
Surface area79630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.806, 221.872, 121.824
Angle α, β, γ (deg.)90.00, 105.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules DFABJKLH

#1: Protein
Methylmalonic aciduria type A protein, mitochondrial


Mass: 38718.867 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMAA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8IVH4, Hydrolases; Acting on acid anhydrides
#2: Protein
Methylmalonyl-CoA mutase, mitochondrial / Methylmalonyl-CoA isomerase


Mass: 83009.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S1PH20, methylmalonyl-CoA mutase

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Non-polymers , 4 types, 25 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Morpheus1-F11 (Molecular Dimensions): 120 mM monosaccharides mix, 100 mM buffer system 3, pH 8.5, 30% precipitant mix 3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→117 Å / Num. obs: 74830 / % possible obs: 89 % / Redundancy: 3.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.092 / Net I/σ(I): 5.2
Reflection shellResolution: 2.794→3.074 Å / Rmerge(I) obs: 0.775 / Num. unique obs: 2737 / CC1/2: 0.562 / Rpim(I) all: 0.504

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WWW

2www


Resolution: 2.79→80.62 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 3731 4.99 %RANDOM
Rwork0.2291 ---
obs0.2315 74782 61.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.79→80.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30209 0 308 13 30530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044362
X-RAY DIFFRACTIONf_angle_d0.6334362
X-RAY DIFFRACTIONf_dihedral_angle_d6.824362
X-RAY DIFFRACTIONf_chiral_restr0.0414889
X-RAY DIFFRACTIONf_plane_restr0.0055440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.830.356990.3873116X-RAY DIFFRACTION3
2.83-2.870.5471100.3908198X-RAY DIFFRACTION5
2.87-2.910.3803160.3368305X-RAY DIFFRACTION7
2.91-2.950.4132140.3884338X-RAY DIFFRACTION8
2.95-2.990.4581250.3719482X-RAY DIFFRACTION11
2.99-3.040.4346290.3698606X-RAY DIFFRACTION14
3.04-3.090.4029560.3559838X-RAY DIFFRACTION20
3.09-3.140.3539470.34321001X-RAY DIFFRACTION24
3.14-3.20.4215840.3421418X-RAY DIFFRACTION33
3.2-3.260.3599940.3141823X-RAY DIFFRACTION43
3.26-3.330.34641260.32372276X-RAY DIFFRACTION54
3.33-3.40.35791280.31582592X-RAY DIFFRACTION61
3.4-3.480.34731490.29892999X-RAY DIFFRACTION70
3.48-3.570.32152170.28843722X-RAY DIFFRACTION88
3.57-3.660.32811950.27914035X-RAY DIFFRACTION95
3.66-3.770.33342340.26194097X-RAY DIFFRACTION98
3.77-3.890.34722280.25414157X-RAY DIFFRACTION98
3.89-4.030.30122220.23744145X-RAY DIFFRACTION97
4.03-4.190.27262070.22514136X-RAY DIFFRACTION97
4.19-4.380.28832060.2074097X-RAY DIFFRACTION96
4.38-4.610.24611840.1934037X-RAY DIFFRACTION94
4.61-4.90.24582290.19183909X-RAY DIFFRACTION92
4.9-5.280.25692120.20843699X-RAY DIFFRACTION87
5.28-5.810.27642080.22154101X-RAY DIFFRACTION96
5.81-6.650.28511960.23274051X-RAY DIFFRACTION94
6.65-8.380.23381880.19973949X-RAY DIFFRACTION92
8.38-80.620.18182180.18073924X-RAY DIFFRACTION91

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