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- PDB-7sek: Solution structure of the zinc finger domain of murine MetAP1, co... -

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Basic information

Entry
Database: PDB / ID: 7sek
TitleSolution structure of the zinc finger domain of murine MetAP1, complexed with ZNG N-terminal peptide
ComponentsCOBW domain-containing protein 1,Methionine aminopeptidase 1 fusion
KeywordsMETAL BINDING PROTEIN / Metallochaperone / zinc finger / COG0523 / METAP1
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / : / methionyl aminopeptidase / metalloaminopeptidase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal / CobW-like, C-terminal domain superfamily / Cobalamin synthesis protein cobW C-terminal domain / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase ...Cobalamin (vitamin B12) biosynthesis CobW-like, C-terminal / CobW-like, C-terminal domain superfamily / Cobalamin synthesis protein cobW C-terminal domain / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Methionine aminopeptidase 1 / COBW domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsEdmonds, K.A. / Jordan, M.R. / Thalluri, K. / Wu, H. / Di Marchi, R. / Giedroc, D.P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118157 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI101171 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM109825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM131994 United States
CitationJournal: Cell / Year: 2022
Title: Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis.
Authors: Weiss, A. / Murdoch, C.C. / Edmonds, K.A. / Jordan, M.R. / Monteith, A.J. / Perera, Y.R. / Rodriguez Nassif, A.M. / Petoletti, A.M. / Beavers, W.N. / Munneke, M.J. / Drury, S.L. / ...Authors: Weiss, A. / Murdoch, C.C. / Edmonds, K.A. / Jordan, M.R. / Monteith, A.J. / Perera, Y.R. / Rodriguez Nassif, A.M. / Petoletti, A.M. / Beavers, W.N. / Munneke, M.J. / Drury, S.L. / Krystofiak, E.S. / Thalluri, K. / Wu, H. / Kruse, A.R.S. / DiMarchi, R.D. / Caprioli, R.M. / Spraggins, J.M. / Chazin, W.J. / Giedroc, D.P. / Skaar, E.P.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COBW domain-containing protein 1,Methionine aminopeptidase 1 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0873
Polymers8,9561
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, inductively coupled plasma mass spectrometry confirms the presence of two zinc ions.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein COBW domain-containing protein 1,Methionine aminopeptidase 1 fusion / Cobalamin synthase W domain-containing protein 1 / MAP 1 / MetAP 1 / Peptidase M 1


Mass: 8956.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbwd1, Metap1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8VEH6, UniProt: Q8BP48, methionyl aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D 1H-15N NOESY
161isotropic13D HN(CA)CO
171isotropic13D HBHA(CO)NH
1111isotropic13D H(CCO)NH
1101isotropic13D C(CO)NH
192isotropic13D (H)CCH-TOCSY
182isotropic13D (H)CCH-TOCSY
1162isotropic12D 1H-13C HSQC aliphatic
1152isotropic22D 1H-13C HSQC aromatic
1142isotropic12D (HB)CB(CGCD)HD
1132isotropic12D (HB)CB(CGCDCE)HE
1121isotropic13d Har(CC-TOCSY-CGCBCACO)NH
1193isotropic12D 1H-13C HSQC CT
1183isotropic12D 1H-13C HSQC CT
1171isotropic12D 1H-15N HSQC long-range
1212isotropic13D 1H-13C NOESY aliphatic
1202isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM [U-13C; U-15N] ZNG-Metap1 fusion, 150 mM sodium chloride, 10 mM sodium phosphate, 2 mM TCEP, 0.3 mM DSS, 90% H2O/10% D2OH2O90% H2O/10% D2O
solution22 mM [U-13C; U-15N] ZNG-Metap1 fusion, 150 mM sodium chloride, 10 mM sodium phosphate, 2 mM TCEP, 0.3 mM DSS, 100% D2OD2O100% D2O
solution32 mM [U-10% 13C; U-100% 15N] ZNG-Metap1 fusion, 150 mM sodium chloride, 10 mM sodium phosphate, 2 mM TCEP, 0.3 mM DSS, 100% D2O10% 13C100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMZNG-Metap1 fusion[U-13C; U-15N]1
150 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
2 mMTCEPnatural abundance1
0.3 mMDSSnatural abundance1
2 mMZNG-Metap1 fusion[U-13C; U-15N]2
150 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
2 mMTCEPnatural abundance2
0.3 mMDSSnatural abundance2
2 mMZNG-Metap1 fusion[U-10% 13C; U-100% 15N]3
150 mMsodium chloridenatural abundance3
10 mMsodium phosphatenatural abundance3
2 mMTCEPnatural abundance3
0.3 mMDSSnatural abundance3
Sample conditionsIonic strength: 150 mM / Label: standard / pH: 7 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298.15 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Varian VNMRSVarianVNMRS8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert P.refinement
CARAKeller and Wuthrichchemical shift assignment
TopSpin4.0.9Bruker Biospincollection
VnmrJVariancollection
NMRFAM-SPARKYNMRFAMdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
hmsISTHyberts, Wagnerprocessing
CYANA3.98.13Guntert P.structure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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