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- PDB-1r9n: Crystal Structure of human dipeptidyl peptidase IV in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1r9n
TitleCrystal Structure of human dipeptidyl peptidase IV in complex with a decapeptide (tNPY) at 2.3 Ang. Resolution
Components
  • Dipeptidyl peptidase IV
  • Neuropeptide Y
KeywordsHYDROLASE / alpha/beta Hydrolase / Eight-bladed beta propeller / Serine Protease
Function / homology
Function and homology information


positive regulation of appetite / adult feeding behavior / glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus ...positive regulation of appetite / adult feeding behavior / glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / neuropeptide hormone activity / feeding behavior / dipeptidyl-peptidase activity / peptide hormone processing / neuronal dense core vesicle / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / neuropeptide signaling pathway / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / G protein-coupled receptor binding / hormone activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / cell adhesion / response to hypoxia / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. ...Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / 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
Dipeptidyl peptidase 4 / Pro-neuropeptide Y
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAertgeerts, K. / Ye, S. / Tennant, M.G. / Collins, B. / Rogers, J. / Sang, B.-C. / Skene, R. / Webb, D.R. / Prasad, G.S.
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal structure of human dipeptidyl peptidase IV in complex with a decapeptide reveals details on substrate specificity and tetrahedral intermediate formation.
Authors: Aertgeerts, K. / Ye, S. / Tennant, M.G. / Kraus, M.L. / Rogers, J. / Sang, B.-C. / Skene, R.J. / Webb, D.R. / Prasad, G.S.
History
DepositionOct 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase IV
E: Neuropeptide Y
B: Dipeptidyl peptidase IV
F: Neuropeptide Y
C: Dipeptidyl peptidase IV
G: Neuropeptide Y
D: Dipeptidyl peptidase IV
H: Neuropeptide Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,42629
Polymers346,9688
Non-polymers5,45821
Water22,5011249
1
A: Dipeptidyl peptidase IV
E: Neuropeptide Y
B: Dipeptidyl peptidase IV
F: Neuropeptide Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,76617
Polymers173,4844
Non-polymers3,28213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint28 kcal/mol
Surface area59970 Å2
MethodPISA
2
C: Dipeptidyl peptidase IV
G: Neuropeptide Y
D: Dipeptidyl peptidase IV
H: Neuropeptide Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,66012
Polymers173,4844
Non-polymers2,1768
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dipeptidyl peptidase IV
G: Neuropeptide Y
hetero molecules

D: Dipeptidyl peptidase IV
H: Neuropeptide Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,66012
Polymers173,4844
Non-polymers2,1768
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8910 Å2
ΔGint8 kcal/mol
Surface area59290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.606, 122.701, 145.405
Angle α, β, γ (deg.)90.00, 114.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103 / Adenosine deaminase complexing protein-2 / ADABP


Mass: 85637.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Plasmid: pFastBacHTb / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Protein/peptide
Neuropeptide Y


Mass: 1104.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: sequence is the same as in the natural source / References: UniProt: Q9XSW6
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 17
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1249 / 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: PEG 2000, Bicine, pH 8.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.3→23270 Å / Num. all: 161260 / Num. obs: 161260 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.054 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.8 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1R9M

1r9m


Resolution: 2.3→41.17 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.164 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 8078 5 %RANDOM
Rwork0.21065 ---
obs0.2127 153134 100 %-
all-161260 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.14 Å20 Å2-1.17 Å2
2--3.08 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24028 0 350 1249 25627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02225120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.94634193
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40652924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60723.9441240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.555154014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.53315120
X-RAY DIFFRACTIONr_chiral_restr0.0930.23640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219254
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.210795
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.216762
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.21125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.2129
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4451.514976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.769223698
X-RAY DIFFRACTIONr_scbond_it1.09311911
X-RAY DIFFRACTIONr_scangle_it1.7084.510495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 625 -
Rwork0.291 11373 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.28640.11480.05010.6428-0.09890.8407-0.0045-0.12180.14890.1446-0.01790.1703-0.0085-0.29560.0224-0.1526-0.00720.004-0.1272-0.0461-0.157111.71130.640819.2922
21.44480.03090.08930.348-0.0720.8065-0.02750.00040.14930.04010.0394-0.16560.05530.1918-0.0118-0.1451-0.002-0.0433-0.1816-0.0675-0.094567.57727.02220.611
32.10430.2434-0.33770.62080.07960.7480.0885-0.2519-0.14280.1257-0.0444-0.21560.10360.4106-0.0441-0.10090.0233-0.0162-0.03450.0016-0.14625.131661.332533.8005
41.27860.1115-0.26870.72110.25991.07780.0581-0.25150.15150.1363-0.08110.4004-0.0948-0.39350.023-0.0214-0.04740.04580.0323-0.04480.016892.881963.01247.2912
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA39 - 76612 - 739
2X-RAY DIFFRACTION2BB36 - 7669 - 739
3X-RAY DIFFRACTION3CC40 - 76613 - 739
4X-RAY DIFFRACTION4DD40 - 76613 - 739

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