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- PDB-5yp4: Crystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pr... -

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Basic information

Entry
Database: PDB / ID: 5yp4
TitleCrystal structure of dipeptidyl peptidase IV (DPP IV) with Lys-Pro from Pseudoxanthomonas mexicana WO24
ComponentsDipeptidyl aminopeptidase 4Dipeptidyl peptidase
KeywordsHYDROLASE / DAP IV / Clan SC S9 / peptidase / DPP4 / DPP8 / DPP9
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / periplasmic space / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LYSINE / PROLINE / Dipeptidyl aminopeptidase 4
Similarity search - Component
Biological speciesPseudoxanthomonas mexicana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoppongi, S. / Suzuki, Y. / Tateoka, C. / Fuimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. ...Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fuimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. / Tanaka, N. / Sakamoto, Y. / Nonaka, T.
Funding support Japan, 10items
OrganizationGrant numberCountry
MEXT16K08322 Japan
MEXT25462872 Japan
MEXT16H04902 Japan
MEXT17H03790 Japan
Protein Institute, Osaka Univ.CR1405, CR1505, CR1605, CR1705 Japan
Protein Institute, Osaka Univ.2013A6822, 2013B 6822, 2014A6924, 2014B6924, 2015A6521, 2015B6521, 2016A6620, 2016B6620, 2017A6721, 2017B6721 Japan
KEK2011G090, 2013G138, 2017G162 Japan
AMED Japan
Takeda Foundation Japan
Nagai Foundation Japan
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Authors: Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fujimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. / Tanaka, N. / Sakamoto, Y. / Nonaka, T.
History
DepositionNov 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl aminopeptidase 4
B: Dipeptidyl aminopeptidase 4
C: Dipeptidyl aminopeptidase 4
D: Dipeptidyl aminopeptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,48533
Polymers329,5024
Non-polymers2,98329
Water51,8292877
1
A: Dipeptidyl aminopeptidase 4
B: Dipeptidyl aminopeptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,56520
Polymers164,7512
Non-polymers1,81418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-17 kcal/mol
Surface area54390 Å2
MethodPISA
2
C: Dipeptidyl aminopeptidase 4
D: Dipeptidyl aminopeptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,92013
Polymers164,7512
Non-polymers1,16911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-18 kcal/mol
Surface area53170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.656, 104.487, 112.838
Angle α, β, γ (deg.)67.42, 68.83, 65.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dipeptidyl aminopeptidase 4 / Dipeptidyl peptidase / Dipeptidyl aminopeptidase IV / DAP IV


Mass: 82375.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoxanthomonas mexicana (bacteria) / Strain: WO24 / Gene: dap4 / Plasmid: pUC19 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q6F3I7, dipeptidyl-peptidase IV
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2877 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidue M12I is mutagenesis according to sequence database UniportKB Q6F3I7 (DAP4_PSEMX).

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 20000, 80mM MES pH6.5, 20% Glycerol, 4mM Lys-Pro

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 245086 / % possible obs: 94.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.073 / Rrim(I) all: 0.11 / Net I/σ(I): 6.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2 / Num. unique obs: 27199 / Rpim(I) all: 0.282 / Rrim(I) all: 0.425 / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia20.5.436data reduction
SCALA3.3.22data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YP1

5yp1


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.336 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 12222 5 %RANDOM
Rwork0.16391 ---
obs0.16635 232846 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.731 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0.84 Å2-0.67 Å2
2---0.34 Å20.74 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22262 0 191 2877 25330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01922990
X-RAY DIFFRACTIONr_bond_other_d0.0060.0221075
X-RAY DIFFRACTIONr_angle_refined_deg1.8871.95931227
X-RAY DIFFRACTIONr_angle_other_deg1.093348683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12552842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52823.0331065
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.269153599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.18815198
X-RAY DIFFRACTIONr_chiral_restr0.1260.23403
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02125812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024974
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0112.04211404
X-RAY DIFFRACTIONr_mcbond_other2.0112.04211404
X-RAY DIFFRACTIONr_mcangle_it2.8463.04714231
X-RAY DIFFRACTIONr_mcangle_other2.8463.04714232
X-RAY DIFFRACTIONr_scbond_it2.7262.34511586
X-RAY DIFFRACTIONr_scbond_other2.7262.34511586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1573.38816996
X-RAY DIFFRACTIONr_long_range_B_refined5.88824.81826233
X-RAY DIFFRACTIONr_long_range_B_other5.84324.67626049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 641 -
Rwork0.215 11640 -
obs--63.73 %

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