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- PDB-4v37: Crystal structure of betaine aldehyde dehydrogenase from spinach ... -

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Basic information

Entry
Database: PDB / ID: 4v37
TitleCrystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with 3-aminopropionaldehyde
ComponentsBETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
KeywordsOXIDOREDUCTASE / BETAINE ALDEHYDE DEHYDROGENASE / ALDH10
Function / homology
Function and homology information


4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / cellular detoxification of aldehyde ...4-trimethylammoniobutyraldehyde dehydrogenase / 4-trimethylammoniobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase activity / aminobutyraldehyde dehydrogenase / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / cellular aldehyde metabolic process / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / cellular detoxification of aldehyde / potassium ion binding / protein homodimerization activity
Similarity search - Function
Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Aldehyde dehydrogenase NAD(P)-dependent / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-aminopropan-1-ol / 2-(2-ETHOXYETHOXY)ETHANOL / FORMIC ACID / : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aminoaldehyde dehydrogenase BADH
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZarate-Romero, A. / Munoz-Clares, R.A.
CitationJournal: To be Published
Title: Identification of a Stable Thiohemiacetal Involving a Conserved Cysteine in the Substrate Inactivation of S. Oleracea Betaine Aldehyde Dehydrogenase
Authors: Zarate-Romero, A. / Mujica-Jimenez, C. / Murillo-Melo, D.S. / Montiel, C. / Munoz-Clares, R.A.
History
DepositionOct 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
B: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
C: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
D: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,07224
Polymers217,1804
Non-polymers3,89220
Water21,2401179
1
A: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
B: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,56612
Polymers108,5902
Non-polymers1,97610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-65.2 kcal/mol
Surface area32090 Å2
MethodPISA
2
C: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
D: BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,50712
Polymers108,5902
Non-polymers1,91710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-61.9 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.296, 80.372, 85.833
Angle α, β, γ (deg.)82.07, 86.40, 79.06
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC


Mass: 54294.965 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17202, betaine-aldehyde dehydrogenase

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Non-polymers , 7 types, 1199 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-0D8 / 3-aminopropan-1-ol


Mass: 75.110 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H9NO
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL / 2-(2-Ethoxyethoxy)ethanol


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1179 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details3-AMINOPROPAN-1-OL (0D8): 3-AMINOPROPAN-1-OL IS COVALENTLY ATTACHED TO THE CYS 450 BY A THIOHEMIACETAL BOND.

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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: 2.03 Å3/Da / Density % sol: 39.39 % / Description: NONE
Crystal growpH: 6.6
Details: AMMONIUM FORMATE 0.2M, POLYETHYLENEGLYCOL 3350 20%., pH 6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078
DetectorType: ADSC Q270 / Detector: CCD / Date: Jul 19, 2014 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.1→24.48 Å / Num. obs: 100653 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.075 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.624 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A0M

4a0m


Resolution: 2.1→24.484 Å / SU ML: 0.2 / σ(F): 1.98 / Phase error: 20.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 5048 5 %
Rwork0.167 --
obs0.1691 100630 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15207 0 250 1179 16636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01416032
X-RAY DIFFRACTIONf_angle_d1.35221855
X-RAY DIFFRACTIONf_dihedral_angle_d14.7995791
X-RAY DIFFRACTIONf_chiral_restr0.392460
X-RAY DIFFRACTIONf_plane_restr0.0072785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0998-2.12370.26631900.22982950X-RAY DIFFRACTION91
2.1237-2.14870.27111880.21853118X-RAY DIFFRACTION96
2.1487-2.17490.2571670.20513160X-RAY DIFFRACTION96
2.1749-2.20240.2751790.20683199X-RAY DIFFRACTION97
2.2024-2.23130.25311410.20423145X-RAY DIFFRACTION96
2.2313-2.26190.25311930.2023164X-RAY DIFFRACTION97
2.2619-2.29420.21771860.19793118X-RAY DIFFRACTION97
2.2942-2.32840.24271580.1983188X-RAY DIFFRACTION97
2.3284-2.36470.24751810.19173186X-RAY DIFFRACTION97
2.3647-2.40350.2411340.19523166X-RAY DIFFRACTION97
2.4035-2.44490.23771690.19673217X-RAY DIFFRACTION97
2.4449-2.48930.24541530.19053156X-RAY DIFFRACTION97
2.4893-2.53710.24431890.19063188X-RAY DIFFRACTION97
2.5371-2.58890.24631370.1863216X-RAY DIFFRACTION97
2.5889-2.64510.24131790.18583179X-RAY DIFFRACTION97
2.6451-2.70650.20451530.18433188X-RAY DIFFRACTION97
2.7065-2.77410.22071770.18113203X-RAY DIFFRACTION97
2.7741-2.8490.23931800.1863209X-RAY DIFFRACTION98
2.849-2.93270.21131650.18023177X-RAY DIFFRACTION98
2.9327-3.02720.22121870.17753174X-RAY DIFFRACTION98
3.0272-3.13520.21951630.17573244X-RAY DIFFRACTION98
3.1352-3.26050.21571600.1753225X-RAY DIFFRACTION98
3.2605-3.40850.23251470.16443250X-RAY DIFFRACTION98
3.4085-3.58770.19561460.15583249X-RAY DIFFRACTION98
3.5877-3.81170.18981880.14533217X-RAY DIFFRACTION98
3.8117-4.10470.1911630.14243206X-RAY DIFFRACTION99
4.1047-4.51550.14191750.12423252X-RAY DIFFRACTION99
4.5155-5.16350.15321610.12063213X-RAY DIFFRACTION99
5.1635-6.48540.17821640.14833237X-RAY DIFFRACTION98
6.4854-24.48590.14611750.12493188X-RAY DIFFRACTION97
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)
10.3179-0.0483-0.00680.6974-0.05060.5790.0070.0343-0.0728-0.0419-0.0384-0.09440.07460.09840.01890.0904-0.0043-0.00090.13390.0050.127139.699620.460739.6361
20.4759-0.1549-0.03630.4235-0.08070.45590.01110.03590.03920.0132-0.0154-0.0477-0.1539-0.01360.0030.1899-0.01910.00190.1384-0.0090.130628.157152.24935.0929
30.70810.21390.0430.3645-0.23841.1046-0.01920.06870.17450.0235-0.0014-0.0241-0.21350.05040.03140.2314-0.02950.00520.13790.00180.208524.543763.9001-8.1892
40.55230.10390.17740.6167-0.00490.6358-0.0139-0.02330.10340.04980.00970.0456-0.0679-0.02660.0040.16470.00290.00760.1377-0.00930.143515.435252.442-3.4612
51.39850.2609-0.05430.92230.00750.8646-0.05820.16790.3036-0.09610.0790.2871-0.2208-0.2761-0.02150.27940.0851-0.02480.29850.05850.3419-8.089862.6941-14.8973
60.6112-0.31430.07240.89280.00260.70260.039-0.00280.00920.11320.00240.13180.0563-0.1002-0.02780.14810.0032-0.00050.1441-0.00390.13354.966240.86050.4616
70.4211-0.3158-0.13561.01090.3550.7675-0.0035-0.04760.01070.15240.0345-0.08360.17050.0402-0.02420.159-0.0088-0.01730.14930.00840.127420.85922.1556-4.1359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 497 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 4 THROUGH 497 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 3 THROUGH 100 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 101 THROUGH 288 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 289 THROUGH 394 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 395 THROUGH 497 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 4 THROUGH 496 )

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