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- PDB-7jxg: Structural model for Fe-containing human acireductone dioxygenase -

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Basic information

Entry
Database: PDB / ID: 7jxg
TitleStructural model for Fe-containing human acireductone dioxygenase
Components1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
KeywordsOXIDOREDUCTASE / cupin barrel / methionine salvage / cancer
Function / homology
Function and homology information


acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / Methionine salvage pathway / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding ...acireductone dioxygenase (Ni2+-requiring) / acireductone dioxygenase [iron(II)-requiring] / acireductone dioxygenase (Ni2+-requiring) activity / acireductone dioxygenase [iron(II)-requiring] activity / Methionine salvage pathway / methionine metabolic process / L-methionine salvage from methylthioadenosine / nickel cation binding / oxidoreductase activity / iron ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Acireductone dioxygenase, eukaryotes / Acireductone dioxygenase ARD family / ARD/ARD' family / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / Acireductone dioxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsNMR-derived with paramagnetic restraints
AuthorsPochapsky, T.C. / Liu, X. / Deshpande, A. / Ringe, D. / Garber, A. / Ryan, J.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM130997
CitationJournal: Biochemistry / Year: 2020
Title: A Model for the Solution Structure of Human Fe(II)-Bound Acireductone Dioxygenase and Interactions with the Regulatory Domain of Matrix Metalloproteinase I (MMP-I).
Authors: Liu, X. / Garber, A. / Ryan, J. / Deshpande, A. / Ringe, D. / Pochapsky, T.C.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5862
Polymers21,5301
Non-polymers561
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area150 Å2
ΔGint-14 kcal/mol
Surface area11020 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase / Acireductone dioxygenase (Fe(2+)-requiring) / Fe-ARD / Membrane-type 1 matrix metalloproteinase ...Acireductone dioxygenase (Fe(2+)-requiring) / Fe-ARD / Membrane-type 1 matrix metalloproteinase cytoplasmic tail-binding protein 1 / MTCBP-1 / Submergence-induced protein-like factor / Sip-L


Mass: 21530.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADI1, MTCBP1, HMFT1638 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BV57, acireductone dioxygenase [iron(II)-requiring]
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11H,15N TROSY-HSQC
121isotropic11H,13C HSQC
131isotropic1HNCA
141isotropic1HN(CO)CA
151isotropic1HN(CA)CB
161isotropic115N-separated NOESY
171isotropic11H,1H NOESY
181isotropic1(H)CCH-TOCSY
191isotropic113C-separated NOESY
2102anisotropic1IPAP 15N-separated TROSY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1400 uM [U-100% 13C; U-100% 15N] human Fe(II)-bound acireductone dioxygenase, 95% H2O/5% D2O13C_15N_sample95% H2O/5% D2O
solution2400 uM [U-15N] human Fe(II)-bound acireductone dioxygenase, 10 mg/mL bacteriophage pf1, 95% H2O/5% D2O15N_sample95% H2O/5% D2OAlignment media added Bacteriophage pf1
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMhuman Fe(II)-bound acireductone dioxygenase[U-100% 13C; U-100% 15N]1
400 uMhuman Fe(II)-bound acireductone dioxygenase[U-15N]2
10 mg/mLbacteriophage pf1none2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.1 Mconditions_17.4 1 atm298 K
20.1 Mconditions_17.4 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker NEO / Manufacturer: Bruker / Model: NEO / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRFAM-SPARKY1.4NMRFAMchemical shift assignment
X-PLOR NIH2.51Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 6

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