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- PDB-5m8p: Crystal structure of human tyrosinase related protein 1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5m8p
TitleCrystal structure of human tyrosinase related protein 1 in complex with tyrosine
Components5,6-dihydroxyindole-2-carboxylic acid oxidase
KeywordsUNKNOWN FUNCTION / human tyrosinase related protein 1 / melanin biosynthesis / tyrosinase / OXIDOREDUCTASE
Function / homology
Function and homology information


acetoacetic acid metabolic process / Melanin biosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanocyte differentiation / melanosome organization / melanosome membrane / intracellular vesicle ...acetoacetic acid metabolic process / Melanin biosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanocyte differentiation / melanosome organization / melanosome membrane / intracellular vesicle / Regulation of MITF-M-dependent genes involved in pigmentation / clathrin-coated endocytic vesicle membrane / melanosome / oxidoreductase activity / endosome membrane / protein homodimerization activity / metal ion binding / cytoplasm
Similarity search - Function
Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / TYROSINE / 5,6-dihydroxyindole-2-carboxylic acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLai, X. / Soler-Lopez, M. / Wichers, H.J. / Dijkstra, B.W.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis.
Authors: Lai, X. / Wichers, H.J. / Soler-Lopez, M. / Dijkstra, B.W.
History
DepositionOct 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details
Revision 2.1Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5,6-dihydroxyindole-2-carboxylic acid oxidase
B: 5,6-dihydroxyindole-2-carboxylic acid oxidase
C: 5,6-dihydroxyindole-2-carboxylic acid oxidase
D: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,12340
Polymers202,4774
Non-polymers12,64636
Water1,17165
1
A: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,42911
Polymers50,6191
Non-polymers2,81010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7919
Polymers50,6191
Non-polymers3,1728
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,90911
Polymers50,6191
Non-polymers3,29010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5,6-dihydroxyindole-2-carboxylic acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9949
Polymers50,6191
Non-polymers3,3758
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.516, 140.322, 191.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 25:85 or (resid 86 and (name...
21(chain C and (resseq 25:85 or (resid 86 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASPASP(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 851 - 61
12ASPASPASPASP(chain A and (resseq 25:85 or (resid 86 and (name...AA8662
13GLNGLNSERSER(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 4701 - 446
14GLNGLNSERSER(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 4701 - 446
15GLNGLNSERSER(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 4701 - 446
16GLNGLNSERSER(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 4701 - 446
17GLNGLNSERSER(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 4701 - 446
18GLNGLNSERSER(chain A and (resseq 25:85 or (resid 86 and (name...AA25 - 4701 - 446
21GLNGLNASPASP(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 851 - 61
22ASPASPASPASP(chain C and (resseq 25:85 or (resid 86 and (name...CC8662
23GLNGLNSERSER(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 4701 - 446
24GLNGLNSERSER(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 4701 - 446
25GLNGLNSERSER(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 4701 - 446
26GLNGLNSERSER(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 4701 - 446
27GLNGLNSERSER(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 4701 - 446
28GLNGLNSERSER(chain C and (resseq 25:85 or (resid 86 and (name...CC25 - 4701 - 446

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
5,6-dihydroxyindole-2-carboxylic acid oxidase / DHICA oxidase / Catalase B / Glycoprotein 75 / Melanoma antigen gp75 / Tyrosinase-related protein 1 / TRP1


Mass: 50619.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TYRP1, CAS2, TYRP, TYRRP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P17643, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor

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Sugars , 10 types, 23 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(5- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(5-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa5-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+2)][a-D-1-deoxy-Tagp]{}}LINUCSPDB-CARE
#10: 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.: 1
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
#13: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 78 molecules

#11: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO3
#12: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris (pH 7.0), 0.2 M NaCl and 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→48.76 Å / Num. obs: 59734 / % possible obs: 99.4 % / Redundancy: 3.4 % / Net I/σ(I): 7.6

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.2data extraction
PHENIX1.10.1_2155refinement
SCALAdata scaling
PHENIXphasing
RefinementResolution: 2.8→47.919 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.55
RfactorNum. reflection% reflection
Rfree0.262 2996 5.02 %
Rwork0.2046 --
obs0.2075 59734 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.92 Å2 / Biso mean: 54.7576 Å2 / Biso min: 20.08 Å2
Refinement stepCycle: final / Resolution: 2.8→47.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14240 0 759 65 15064
Biso mean--77.46 41.5 -
Num. residues----1788
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4176X-RAY DIFFRACTION7.833TORSIONAL
12C4176X-RAY DIFFRACTION7.833TORSIONAL

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