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- PDB-2cg5: Structure of aminoadipate-semialdehyde dehydrogenase- phosphopant... -

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Basic information

Entry
Database: PDB / ID: 2cg5
TitleStructure of aminoadipate-semialdehyde dehydrogenase- phosphopantetheinyl transferase in complex with cytosolic acyl carrier protein and coenzyme A
Components
  • FATTY ACID SYNTHASE
  • L-AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE-PHOSPHOPANTETHEINYL TRANSFERASE
KeywordsTRANSFERASE/HYDROLASE / TRANSFERASE-HYDROLASE COMPLEX / TRANSFERASE-HYDROLASE (COMPLEX) / FATTY ACID BIOSYNTHESIS / PHOSPHOPANTETHEINE TRANSFERASE / FASN / ACP / COENZYME A / TRANSFERASE / HYDROLASE / LIPID SYNTHESIS / LYASE / COMPLEX
Function / homology
Function and homology information


pantothenate metabolic process / 10-formyltetrahydrofolate catabolic process / holo-[acyl-carrier-protein] synthase / fatty-acid synthase system / ether lipid biosynthetic process / lysine biosynthetic process via aminoadipic acid / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / fatty-acyl-CoA biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) ...pantothenate metabolic process / 10-formyltetrahydrofolate catabolic process / holo-[acyl-carrier-protein] synthase / fatty-acid synthase system / ether lipid biosynthetic process / lysine biosynthetic process via aminoadipic acid / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / fatty-acyl-CoA biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / establishment of endothelial intestinal barrier / glycogen granule / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / Fatty acyl-CoA biosynthesis / host-mediated perturbation of viral process / ChREBP activates metabolic gene expression / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / acetyl-CoA metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / mammary gland development / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / fatty acid synthase activity / monocyte differentiation / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to nutrient / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / protein maturation / fatty acid metabolic process / osteoblast differentiation / fatty acid biosynthetic process / melanosome / cadherin binding / inflammatory response / magnesium ion binding / Golgi apparatus / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / 4'-phosphopantetheinyl transferase, N-terminal / : / 4'-phosphopantetheinyl transferase domain / : / Fatty acid synthase, pseudo-KR domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Methyltransferase type 12 ...: / 4'-phosphopantetheinyl transferase, N-terminal / : / 4'-phosphopantetheinyl transferase domain / : / Fatty acid synthase, pseudo-KR domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Methyltransferase type 12 / Methyltransferase domain / Ribosomal Protein L22; Chain A / Thioesterase / Thioesterase domain / ACP-like / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / NICKEL (II) ION / PHOSPHATE ION / Fatty acid synthase / L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBunkoczi, G. / Joshi, A. / Papagrigoriu, E. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / von Delft, F. / Smith, S. / Oppermann, U.
CitationJournal: Chem.Biol. / Year: 2007
Title: Mechanism and Substrate Recognition of Human Holo Acp Synthase.
Authors: Bunkoczi, G. / Pasta, S. / Joshi, A. / Wu, X. / Kavanagh, K.L. / Smith, S. / Oppermann, U.
History
DepositionFeb 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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 / struct_conn
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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE-PHOSPHOPANTETHEINYL TRANSFERASE
B: FATTY ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0877
Polymers47,1172
Non-polymers9705
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.361, 69.361, 184.715
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein L-AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE-PHOSPHOPANTETHEINYL TRANSFERASE / 4'-PHOSPHOPANTETHEINYL TRANSFERASE / ALPHA- AMINOADIPIC SEMIALDEHYDE DEHYDROGENASE- ...4'-PHOSPHOPANTETHEINYL TRANSFERASE / ALPHA- AMINOADIPIC SEMIALDEHYDE DEHYDROGENASE- PHOSPHOPANTETHEINYL TRANSFERASE / AASD-PPT / LYS5 ORTHOLOG


Mass: 37051.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOEX-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9NRN7, L-aminoadipate-semialdehyde dehydrogenase
#2: Protein FATTY ACID SYNTHASE / ACYL-CARRIER-PROTEIN


Mass: 10065.395 Da / Num. of mol.: 1 / Fragment: ACP DOMAIN, RESIDUES 2119-2207 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49327, fatty-acid synthase system

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Non-polymers , 5 types, 29 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, SER 2156 TO ALA

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growDetails: 0.4 M (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 12, 2006 / Details: MIRRORS
RadiationMonochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→34.7 Å / Num. obs: 14864 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYD

2byd


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 22.568 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.481 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 732 4.9 %RANDOM
Rwork0.192 ---
obs0.195 14089 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20.72 Å20 Å2
2--1.43 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 46 24 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222743
X-RAY DIFFRACTIONr_bond_other_d0.0010.021834
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.973730
X-RAY DIFFRACTIONr_angle_other_deg0.87134455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10123.445119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13815445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5371519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined0.2330.2698
X-RAY DIFFRACTIONr_nbd_other0.2010.22085
X-RAY DIFFRACTIONr_nbtor_refined0.20.21368
X-RAY DIFFRACTIONr_nbtor_other0.0930.21571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5061.51724
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89622706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.28731149
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1144.51023
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: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 62
Rwork0.32 1012
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)
14.11361.2006-0.35864.0262-0.02743.88860.0469-0.07980.21940.05450.1486-0.2452-0.3710.2459-0.19550.1397-0.3011-0.1153-0.36530.0773-0.1646-24.232917.8985.1532
22.2311.3534-0.11176.05491.50324.24310.1069-0.12560.31510.6121-0.01540.7342-0.2032-0.5533-0.09140.1849-0.2111-0.0112-0.20380.0648-0.0813-45.05159.309915.8301
38.1749-4.32752.52847.2306-1.70193.6648-0.2277-0.2038-0.92430.2230.3165-0.34110.93620.2082-0.08880.3727-0.1123-0.1309-0.13250.02110.0647-26.389-12.579415.6774
41.6901-0.6199-0.82130.4682-1.201510.1955-0.5037-0.2077-0.20720.8330.1804-0.5487-0.15210.03010.32330.4259-0.1488-0.2139-0.18520.0903-0.0877-29.609-3.505122.3092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 133
2X-RAY DIFFRACTION1A276 - 299
3X-RAY DIFFRACTION2A134 - 259
4X-RAY DIFFRACTION3B2124 - 2149
5X-RAY DIFFRACTION3B2183 - 2194
6X-RAY DIFFRACTION4B2150 - 2182

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