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- PDB-2wm1: The crystal structure of human alpha-amino-beta-carboxymuconate- ... -

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Basic information

Entry
Database: PDB / ID: 2wm1
TitleThe crystal structure of human alpha-amino-beta-carboxymuconate- epsilon-semialdehyde decarboxylase in complex with 1,3- dihydroxyacetonephosphate suggests a regulatory link between NAD synthesis and glycolysis
Components2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
KeywordsLYASE / NEUROLOGICAL DISORDERS / METAL-DEPENDENT AMIDOHYDROLASE / KYNURENINE PATHWAY / ALTERNATIVE SPLICING / QUINOLINIC ACID / NAD BIOSYNTHESIS / CEREBRAL MALARIA / DECARBOXYLASE / PICOLINIC ACID / PHOSPHOPROTEIN
Function / homology
Function and homology information


aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from L-tryptophan / aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / L-tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding ...aminocarboxymuconate-semialdehyde decarboxylase activity / negative regulation of quinolinate biosynthetic process / picolinic acid biosynthetic process / regulation of 'de novo' NAD biosynthetic process from L-tryptophan / aminocarboxymuconate-semialdehyde decarboxylase / secondary metabolic process / L-tryptophan catabolic process / Tryptophan catabolism / hydrolase activity / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsGaravaglia, S. / Perozzi, S. / Galeazzi, L. / Raffaelli, N. / Rizzi, M.
CitationJournal: FEBS J. / Year: 2009
Title: The Crystal Structure of Human Alpha-Amino-Beta-Carboxymuconate-Epsilon-Semialdehyde Decarboxylase in Complex with 1,3-Dihydroxyacetonephosphate Suggests a Regulatory Link between Nad Synthesis and Glycolysis
Authors: Garavaglia, S. / Perozzi, S. / Galeazzi, L. / Raffaelli, N. / Rizzi, M.
History
DepositionJun 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4124
Polymers38,0841
Non-polymers3283
Water3,891216
1
A: 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
hetero molecules

A: 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8248
Polymers76,1682
Non-polymers6556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area6330 Å2
ΔGint-122.5 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.227, 86.227, 92.168
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE / ALPHA-AMINO-BETA-CARBOXYMUCONATE-EPSILON-SEMIALDEHYDE DECARBOXYLASE


Mass: 38084.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): GS115 / Production host: PICHIA PASTORIS (fungus)
References: UniProt: Q8TDX5, aminocarboxymuconate-semialdehyde decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsLAST FOUR C-TERMINAL RESIDUES NOT VISIBLE IN THE ELECTRON DENSITY

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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 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24525 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.8 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HBV

2hbv


Resolution: 2.01→43.11 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.867 / SU B: 4.161 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25674 1766 7.2 %RANDOM
Rwork0.19288 ---
obs0.19754 22727 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.672 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.01→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 17 216 2868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9743679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2424.138116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06915477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg221513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212042
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8651.51654
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51922668
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57731066
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9944.51011
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 128 -
Rwork0.193 1669 -
obs--100 %

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