[English] 日本語
Yorodumi
- PDB-7ud6: Designed Enzyme SH3-588 (Catechol O-methyltransferase catalytic d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ud6
TitleDesigned Enzyme SH3-588 (Catechol O-methyltransferase catalytic domain and Src homology 3 binding domain fusion)
ComponentsTyrosine-protein kinase Fyn,Catechol O-methyltransferase
KeywordsTRANSFERASE / Designed enzyme / COMT / SH3 / fusion protein
Function / homology
Function and homology information


positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process ...positive regulation of homocysteine metabolic process / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / negative regulation of dopamine metabolic process / S-adenosylmethionine metabolic process / renin secretion into blood stream / dopamine secretion / catecholamine metabolic process / renal albumin absorption / habituation / artery development / short-term memory / cerebellar cortex morphogenesis / response to salt / dopamine catabolic process / glomerulus development / norepinephrine metabolic process / fear response / synaptic transmission, dopaminergic / cellular response to phosphate starvation / response to angiotensin / cellular response to cocaine / estrogen metabolic process / exploration behavior / cholesterol efflux / response to food / prostaglandin metabolic process / response to corticosterone / response to temperature stimulus / response to pain / glycogen metabolic process / response to stress / startle response / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to cytokine / learning / kidney development / female pregnancy / negative regulation of smooth muscle cell proliferation / : / visual learning / multicellular organism growth / regulation of blood pressure / memory / response to wounding / cognition / response to estrogen / response to toxic substance / cell body / gene expression / methylation / vesicle / dendritic spine / response to oxidative stress / response to lipopolysaccharide / postsynaptic membrane / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Fyn/Yrk, SH3 domain / Grb2-like / Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains ...Fyn/Yrk, SH3 domain / Grb2-like / Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / FYN proto-oncogene, Src family tyrosine kinase / Catechol O-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsOngpipattanakul, C. / Nair, S.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Designer installation of a substrate recruitment domain to tailor enzyme specificity.
Authors: Park, R. / Ongpipattanakul, C. / Nair, S.K. / Bowers, A.A. / Kuhlman, B.
History
DepositionMar 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein kinase Fyn,Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0583
Polymers32,6341
Non-polymers4242
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.883, 68.883, 302.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Tyrosine-protein kinase Fyn,Catechol O-methyltransferase


Mass: 32634.008 Da / Num. of mol.: 1
Mutation: Q26V,N29R,E37L,R39V,R73E,Y74F,Q77L,N78V,T93Q,Q97Y,K98R
Source method: isolated from a genetically manipulated source
Details: The enzyme is a fusion between COMT from Rattus norvegicus and the SH3 domain from Homo sapiens.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: FYN, Comt / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E5RFS5, UniProt: P22734, catechol O-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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsCOMT domain in 7UD6 was designed using PDB ID: 5P9V as a template. 5P9V contains two humanizing ...COMT domain in 7UD6 was designed using PDB ID: 5P9V as a template. 5P9V contains two humanizing mutations, Ile153 and Cys157 (7UD6 numbering), which are not present in Uniprot ID: P22734. Additional engineered residues present in 7UD6 were computationally designed to enhance interactions between the COMT and SH3 domains

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7 M magnesium formate, 0.1 M bis-tris propone pH 7.0.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.59→59.654 Å / Num. obs: 14097 / % possible obs: 99.6 % / Redundancy: 27.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.021 / Rrim(I) all: 0.11 / Net I/σ(I): 26.3
Reflection shellResolution: 2.594→2.602 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 140 / CC1/2: 0.923 / Rpim(I) all: 0.297 / Rrim(I) all: 1.394 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M27, 4PYN

1m27

4pyn


Resolution: 2.59→55.5 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 671 4.78 %
Rwork0.2466 --
obs0.2483 14038 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 1 2 2098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092138
X-RAY DIFFRACTIONf_angle_d1.4592901
X-RAY DIFFRACTIONf_dihedral_angle_d14.563299
X-RAY DIFFRACTIONf_chiral_restr0.071327
X-RAY DIFFRACTIONf_plane_restr0.012368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.790.38741110.33522593X-RAY DIFFRACTION99
2.79-3.070.3991400.30612590X-RAY DIFFRACTION100
3.08-3.520.33141470.28012619X-RAY DIFFRACTION99
3.52-4.430.22371250.23582655X-RAY DIFFRACTION98
4.43-55.50.25681480.21972910X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.1947 Å / Origin y: 30.3494 Å / Origin z: -27.0127 Å
111213212223313233
T1.008 Å2-0.2398 Å20.2008 Å2-0.4704 Å2-0.0006 Å2--0.6154 Å2
L0.4692 °2-0.0732 °2-0.5851 °2-1.5495 °2-1.1233 °2--1.9904 °2
S0.4842 Å °0.2346 Å °0.0031 Å °0.6519 Å °0.0546 Å °0.1711 Å °-1.2402 Å °0.3535 Å °0.2779 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more