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- PDB-6gfo: cyanobacterial GAPDH with full-length CP12 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6gfo
Titlecyanobacterial GAPDH with full-length CP12
Components
  • CP12 polypeptide
  • Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 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 / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding / nucleotide binding
Similarity search - Function
Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / 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 ...Calvin cycle protein CP12-like / CP12 domain / CP12 domain / CP12 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / CP12 polypeptide / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
E: CP12 polypeptide
F: CP12 polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,14311
Polymers164,3936
Non-polymers2,7505
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25020 Å2
ΔGint-173 kcal/mol
Surface area49720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.446, 141.049, 81.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase


Mass: 36792.734 Da / Num. of mol.: 4
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 his-tag variant / 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: Protein CP12 polypeptide


Mass: 8611.127 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: cp12 / Plasmid: pRSETA / Details (production host): thrombin his-tag variant / Production host: Escherichia coli KRX (bacteria) / References: UniProt: Q8DHX3
#3: 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
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.42 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 1% Tryptone, 0.001 M Azide, 0.005 M Azide, 12 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→70.63 Å / Num. obs: 92479 / % possible obs: 99.94 % / Redundancy: 6.3 % / Biso Wilson estimate: 26.8 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.1387 / Rpim(I) all: 0.0601 / Rrim(I) all: 0.1514 / Net I/σ(I): 6.9
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.4962 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 9129 / CC1/2: 0.905 / Rrim(I) all: 0.5416 / % possible all: 99.91

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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: 2.1→70.627 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 23.01
RfactorNum. reflection% reflection
Rfree0.2185 4599 4.97 %
Rwork0.1707 --
obs0.1731 92473 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→70.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11426 0 181 338 11945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711874
X-RAY DIFFRACTIONf_angle_d0.90516172
X-RAY DIFFRACTIONf_dihedral_angle_d7.2719398
X-RAY DIFFRACTIONf_chiral_restr0.0551842
X-RAY DIFFRACTIONf_plane_restr0.0062084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0995-2.12340.26321530.2262866X-RAY DIFFRACTION99
2.1234-2.14840.29621450.22382928X-RAY DIFFRACTION100
2.1484-2.17460.27081550.20932869X-RAY DIFFRACTION100
2.1746-2.20210.26561400.21752925X-RAY DIFFRACTION100
2.2021-2.23110.25871510.20332858X-RAY DIFFRACTION100
2.2311-2.26170.26241630.19842906X-RAY DIFFRACTION100
2.2617-2.2940.25881660.18532876X-RAY DIFFRACTION100
2.294-2.32820.2681560.19512895X-RAY DIFFRACTION100
2.3282-2.36460.28421550.19252893X-RAY DIFFRACTION100
2.3646-2.40340.2681620.18352883X-RAY DIFFRACTION100
2.4034-2.44480.22941600.1822896X-RAY DIFFRACTION100
2.4448-2.48930.25581530.17932913X-RAY DIFFRACTION100
2.4893-2.53720.26491640.18132866X-RAY DIFFRACTION100
2.5372-2.58890.24841520.18482916X-RAY DIFFRACTION100
2.5889-2.64520.23911410.17912923X-RAY DIFFRACTION100
2.6452-2.70680.23011320.17812921X-RAY DIFFRACTION100
2.7068-2.77450.23341480.17922929X-RAY DIFFRACTION100
2.7745-2.84950.24641550.18242929X-RAY DIFFRACTION100
2.8495-2.93330.24911420.19452923X-RAY DIFFRACTION100
2.9333-3.0280.22131310.18472963X-RAY DIFFRACTION100
3.028-3.13620.23091570.18612926X-RAY DIFFRACTION100
3.1362-3.26180.2211430.1792955X-RAY DIFFRACTION100
3.2618-3.41030.21141570.17462920X-RAY DIFFRACTION100
3.4103-3.59010.2171470.15942946X-RAY DIFFRACTION100
3.5901-3.8150.1981770.15972928X-RAY DIFFRACTION100
3.815-4.10950.18961500.14562961X-RAY DIFFRACTION100
4.1095-4.5230.15281520.12463004X-RAY DIFFRACTION100
4.523-5.17730.16831410.13562981X-RAY DIFFRACTION100
5.1773-6.52210.23681530.16553048X-RAY DIFFRACTION100
6.5221-70.66690.18151980.16813127X-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)
13.6402-0.24811.05493.683-0.56192.2267-0.02340.1942-0.0184-0.2371-0.0738-0.17040.13730.15420.09050.2070.02090.07850.2130.02290.211648.286939.723564.8075
23.11830.2814-2.41383.0473-2.44783.8417-0.09610.19010.1085-0.3584-0.0969-0.49270.26030.12980.17830.2133-0.00410.03950.2702-0.00040.285153.465740.772165.6498
32.8983-0.5209-0.0711.0608-0.29281.1210.0180.23480.418-0.182-0.0142-0.1537-0.02160.0585-0.02310.2460.00240.01570.17860.05140.234634.352555.130963.4165
43.68850.71040.2021.39431.44334.29620.0520.4640.633-0.3371-0.06-0.5318-0.3190.22910.12030.2684-0.0069-0.02040.27210.04930.350140.342153.957887.386
50.37340.1135-0.09330.7685-0.3090.5156-0.04340.17350.2017-0.0676-0.01590-0.08950.05280.05030.16540.00910.00770.17660.03580.238224.495554.22775.187
62.9365-0.2546-0.75081.13860.20.97390.00680.17080.0526-0.14560.02340.04280.0362-0.1136-0.05080.18880.004-0.03010.17060.01450.183523.618942.916366.8851
72.1708-0.00720.19413.9437-1.12551.5871-0.02990.1499-0.2147-0.29920.00170.23250.1211-0.12970.01810.2167-0.0123-0.01010.1842-0.05310.213122.636111.656384.9525
80.9221-0.2576-0.05870.3081-0.04540.2983-0.015-0.0377-0.14250.0528-0.0443-0.16080.07070.01390.05410.2187-0.0041-0.01230.1990.03260.291944.785216.632994.0179
91.3641-0.15770.2121.8109-0.93431.31460.0794-0.3219-0.00590.34430.06220.2134-0.0751-0.1141-0.1210.2759-0.00390.04360.2991-0.05040.205611.398143.1957109.9839
100.6808-0.1768-0.13250.96980.30360.58660.0061-0.01520.17620.0463-0.00230.0658-0.0499-0.07430.00890.15280.00030.01170.17790.00080.205616.779953.215792.0565
111.8242-0.7670.60911.4625-0.03031.7427-0.1176-0.18340.90710.3274-0.1304-0.9237-0.31330.15480.19260.3635-0.0893-0.18670.2806-0.02390.831655.429659.1884103.5033
121.2482-0.42230.50271.228-0.50720.8421-0.056-0.25430.07750.3176-0.0633-0.3826-0.07120.1430.04770.2536-0.0291-0.11490.25750.00770.33652.018535.719107.1273
132.84132.63930.23439.16342.54862.6464-0.24410.0369-0.86280.12380.4225-0.4464-0.00930.3091-0.16090.54720.1659-0.00031.13370.00311.057273.426969.726870.0243
143.3442-3.4173-0.77328.19140.90141.89890.094-0.1995-0.10640.471-0.47370.41630.3651-0.2960.21620.60890.07790.0421.00290.28811.177773.05759.896777.0583
157.4467-0.2823-4.10614.52520.23723.00470.29240.1783-0.11950.2858-0.4671-0.7961-0.5850.9105-0.10290.3661-0.0333-0.05820.48420.10780.797660.313346.861883.8377
168.79445.52160.48349.4876-0.51996.15870.196-0.2165-0.0855-0.0436-0.26790.46990.6963-0.4151-0.06940.5280.0011-0.04890.5585-0.0440.308819.623332.3963132.1286
174.22965.03070.42475.90120.5216.4089-0.1756-0.2042-1.03240.16710.0847-0.79771.0602-0.28540.07460.6844-0.01430.0420.45240.00080.473226.123929.0807137.2272
182.52151.3359-2.34444.6105-3.28273.2281-0.0279-0.7932-0.55960.1823-0.1452-0.27220.8535-0.55140.02710.5665-0.03480.08280.55340.10210.505417.560419.0139114.2053
197.7364-0.533-4.0236.58390.96249.4795-0.3794-0.2574-0.43890.0044-0.011-0.16130.6518-0.31260.34440.3815-0.03690.00910.19590.02510.345925.103821.1381101.0592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 202 )
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 255 )
6X-RAY DIFFRACTION6chain 'A' and (resid 256 through 337 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 132 )
8X-RAY DIFFRACTION8chain 'B' and (resid 133 through 337 )
9X-RAY DIFFRACTION9chain 'C' and (resid 0 through 170 )
10X-RAY DIFFRACTION10chain 'C' and (resid 171 through 337 )
11X-RAY DIFFRACTION11chain 'D' and (resid 0 through 153 )
12X-RAY DIFFRACTION12chain 'D' and (resid 154 through 337 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 26 )
14X-RAY DIFFRACTION14chain 'E' and (resid 27 through 52 )
15X-RAY DIFFRACTION15chain 'E' and (resid 53 through 75 )
16X-RAY DIFFRACTION16chain 'F' and (resid 2 through 22 )
17X-RAY DIFFRACTION17chain 'F' and (resid 23 through 45 )
18X-RAY DIFFRACTION18chain 'F' and (resid 46 through 63 )
19X-RAY DIFFRACTION19chain 'F' and (resid 64 through 75 )

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