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- PDB-6gfr: cyanobacterial GAPDH with NAD -

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Basic information

Entry
Database: PDB / ID: 6gfr
Titlecyanobacterial GAPDH with NAD
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsPHOTOSYNTHESIS / Calvin Cycle / Regulation
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding / metal ion binding / cytosol
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.919 Å
AuthorsMcFarlane, C.R. / Murray, J.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014575/1 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural basis of light-induced redox regulation in the Calvin-Benson cycle in cyanobacteria.
Authors: Ciaran R McFarlane / Nita R Shah / Burak V Kabasakal / Blanca Echeverria / Charles A R Cotton / Doryen Bubeck / James W Murray /
Abstract: Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin-Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential ...Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin-Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential CB-cycle enzymes that control substrate availability for the carboxylation enzyme Rubisco. PRK consumes ATP to produce the Rubisco substrate ribulose bisphosphate (RuBP). GAPDH catalyzes the reduction step of the CB cycle with NADPH to produce the sugar glyceraldehyde 3-phosphate (GAP), which is used for regeneration of RuBP and is the main exit point of the cycle. GAPDH and PRK are coregulated by the redox state of a conditionally disordered protein CP12, which forms a ternary complex with both enzymes. However, the structural basis of CB-cycle regulation by CP12 is unknown. Here, we show how CP12 modulates the activity of both GAPDH and PRK. Using thermophilic cyanobacterial homologs, we solve crystal structures of GAPDH with different cofactors and CP12 bound, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide preorders CP12 prior to binding the PRK active site, which is resolved in complex with CP12. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our structural and biochemical data explain how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation.
History
DepositionMay 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1148
Polymers73,5852
Non-polymers1,5286
Water7,044391
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,22816
Polymers147,1714
Non-polymers3,05712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area21080 Å2
ΔGint-154 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.865, 139.865, 80.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1276-

HOH

21B-1257-

HOH

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 36792.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tll1466 / Plasmid: pRSETA / Details (production host): thrombin cleavable his-tag / Production host: Escherichia coli KRX (bacteria)
References: UniProt: Q8DIW5, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.69 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: 12% PEG3350 2% Tacsimate, 100 mM Hepes, pH 7

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.919→69.93 Å / Num. obs: 61333 / % possible obs: 99.88 % / Redundancy: 12.9 % / Biso Wilson estimate: 24.85 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.2205 / Rrim(I) all: 0.2297 / Net I/σ(I): 7.94
Reflection shellResolution: 1.919→1.988 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.9235 / Mean I/σ(I) obs: 2.03 / CC1/2: 0.543 / Rrim(I) all: 0.9625 / % possible all: 99.08

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BOY

4boy


Resolution: 1.919→69.93 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.09
RfactorNum. reflection% reflection
Rfree0.2063 3050 4.97 %
Rwork0.1648 --
obs0.1669 61317 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.919→69.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 101 391 5646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075368
X-RAY DIFFRACTIONf_angle_d0.9027312
X-RAY DIFFRACTIONf_dihedral_angle_d13.753187
X-RAY DIFFRACTIONf_chiral_restr0.056841
X-RAY DIFFRACTIONf_plane_restr0.006932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9187-1.94870.31921250.30562522X-RAY DIFFRACTION97
1.9487-1.98070.33731360.28522604X-RAY DIFFRACTION100
1.9807-2.01480.29131300.25972631X-RAY DIFFRACTION100
2.0148-2.05150.27651380.24592603X-RAY DIFFRACTION100
2.0515-2.09090.26541510.22982618X-RAY DIFFRACTION100
2.0909-2.13360.25971410.21092598X-RAY DIFFRACTION100
2.1336-2.180.22791350.2042650X-RAY DIFFRACTION100
2.18-2.23070.24011450.1882594X-RAY DIFFRACTION100
2.2307-2.28650.21761470.18432595X-RAY DIFFRACTION100
2.2865-2.34830.24741440.17362642X-RAY DIFFRACTION100
2.3483-2.41750.24111300.16732624X-RAY DIFFRACTION100
2.4175-2.49550.19911320.16762643X-RAY DIFFRACTION100
2.4955-2.58470.211180.16862661X-RAY DIFFRACTION100
2.5847-2.68820.23971230.16642672X-RAY DIFFRACTION100
2.6882-2.81050.21311300.15672649X-RAY DIFFRACTION100
2.8105-2.95870.1981380.1662647X-RAY DIFFRACTION100
2.9587-3.14410.20521540.1652648X-RAY DIFFRACTION100
3.1441-3.38680.20791390.15472671X-RAY DIFFRACTION100
3.3868-3.72760.17221410.13742683X-RAY DIFFRACTION100
3.7276-4.2670.17171720.12692679X-RAY DIFFRACTION100
4.267-5.37560.16511480.12012743X-RAY DIFFRACTION100
5.3756-69.97910.17551330.15472890X-RAY DIFFRACTION100
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)
13.0870.5705-0.22292.68530.40431.314-0.07140.2204-0.1999-0.20220.0955-0.31260.1060.1817-0.01310.17980.01510.04970.1986-0.02150.1536-14.6073-52.5033-14.0164
20.99520.1688-0.17110.9249-0.09720.4685-0.01640.05350.1126-0.14640.0075-0.212-0.05870.11450.00720.1746-0.02550.01630.16850.03070.2163-18.7494-29.5253-8.5279
33.3746-0.34841.68640.47-1.00873.19210.0530.54690.2078-0.6674-0.0762-0.0257-0.32110.20170.0530.49610.044-0.0940.33980.07780.2224-48.5775-29.688-25.5825
40.9358-0.199-0.13633.073-0.88921.38980.02970.28490.1097-0.286-0.04720.6975-0.272-0.26320.00230.31680.098-0.18530.3866-0.02070.384-64.8863-36.5887-20.7877
51.73451.70.82233.21882.3211.8078-0.03290.0443-0.0192-0.1831-0.10770.3997-0.0899-0.11460.17180.15250.0263-0.04160.15530.00840.2018-56.197-40.6686-0.8215
63.95350.71442.35861.9922.32124.382-0.1460.0520.2563-0.3271-0.33660.5929-0.2443-0.4580.49650.19210.037-0.0450.1961-0.00250.2978-62.6181-47.3625-5.9042
71.15520.4104-0.16063.0806-0.11431.2144-0.03550.0745-0.2186-0.0847-0.09460.36870.0476-0.09320.13510.11940.0097-0.0260.1557-0.01680.2325-56.7705-54.5869-5.5852
81.29610.0058-0.0512.3634-0.61051.7706-0.03250.2964-0.2016-0.3482-0.0470.15570.0485-0.09210.04140.17940.0125-0.05550.2215-0.05940.2152-52.7621-54.3462-17.4374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 337 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 72 )
4X-RAY DIFFRACTION4chain 'B' and (resid 73 through 170 )
5X-RAY DIFFRACTION5chain 'B' and (resid 171 through 202 )
6X-RAY DIFFRACTION6chain 'B' and (resid 203 through 228 )
7X-RAY DIFFRACTION7chain 'B' and (resid 229 through 255 )
8X-RAY DIFFRACTION8chain 'B' and (resid 256 through 337 )

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