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- PDB-1xcj: Guanidinoacetate methyltransferase containing S-adenosylhomocyste... -

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Basic information

Entry
Database: PDB / ID: 1xcj
TitleGuanidinoacetate methyltransferase containing S-adenosylhomocysteine and guanidinoacetate
ComponentsGuanidinoacetate N-methyltransferase
KeywordsTRANSFERASE / Guanidinoacetate methyltransferase / Methyltransferase / S-adenosylhomocysteine / guanidinoacetate
Function / homology
Function and homology information


Creatine metabolism / guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine biosynthetic process / embryonic liver development / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / animal organ morphogenesis ...Creatine metabolism / guanidinoacetate N-methyltransferase / guanidinoacetate N-methyltransferase activity / creatine biosynthetic process / embryonic liver development / S-adenosylhomocysteine metabolic process / S-adenosylmethionine metabolic process / S-adenosylmethionine-dependent methyltransferase activity / regulation of multicellular organism growth / animal organ morphogenesis / spermatogenesis / methylation / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Guanidinoacetate N-methyltransferase / Arginine N-methyltransferase 2-like domain / : / Arginine and arginine-like N-methyltransferase domain profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANIDINO ACETATE / S-ADENOSYL-L-HOMOCYSTEINE / Guanidinoacetate N-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKomoto, J. / Yamada, T. / Takata, Y. / Takusagawa, F.
CitationJournal: Biochemistry / Year: 2004
Title: Catalytic mechanism of guanidinoacetate methyltransferase: crystal structures of guanidinoacetate methyltransferase ternary complexes.
Authors: Komoto, J. / Yamada, T. / Takata, Y. / Konishi, K. / Ogawa, H. / Gomi, T. / Fujioka, M. / Takusagawa, F.
History
DepositionSep 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The author states that residue 119 is indeed a Val instead of Glu. There is an error in ...SEQUENCE The author states that residue 119 is indeed a Val instead of Glu. There is an error in the original published sequence (Proc. Natl. Acad. Sci. USA 85, 694-698 (1988)).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanidinoacetate N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7763
Polymers26,2741
Non-polymers5022
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.188, 41.403, 42.320
Angle α, β, γ (deg.)104.25, 112.67, 104.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Guanidinoacetate N-methyltransferase


Mass: 26274.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: Liver / Gene: gamt / Plasmid: pUCGAT9-1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P10868, guanidinoacetate N-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-NMG / GUANIDINO ACETATE / N-[AMINO(IMINO)METHYL]GLYCINE


Mass: 117.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 8% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: Confocal
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 12785 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 / Rsym value: 0.038
Reflection shellResolution: 2→2.07 Å / % possible all: 74

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 1310 RANDOM
Rwork0.224 --
all0.225 12785 -
obs0.225 12785 -
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 34 60 1910

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