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- PDB-7o54: Crystal structure of the carbonic anhydrase-like domain of CcmM i... -

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Basic information

Entry
Database: PDB / ID: 7o54
TitleCrystal structure of the carbonic anhydrase-like domain of CcmM in complex with the C-terminal 17 residues of CcaA from Synechococcus elongatus (strain PCC 7942)
Components
  • Carbonic anhydrase
  • Carboxysome assembly protein CcmM
KeywordsPHOTOSYNTHESIS / protein binding carboxysome
Function / homology
Function and homology information


structural constituent of carboxysome shell / carbon utilization / carboxysome / carbon fixation / photosynthesis / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carboxysome assembly protein CcmM / : / Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / Ribulose bisphosphate carboxylase small subunit, domain ...Carboxysome assembly protein CcmM / : / Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Carbonic anhydrase / Carboxysome assembly protein CcmM
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZang, K. / Wang, H. / Hartl, F.U. / Hayer-Hartl, M.
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis.
Authors: Kun Zang / Huping Wang / F Ulrich Hartl / Manajit Hayer-Hartl /
Abstract: Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural ...Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxysome assembly protein CcmM
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3204
Polymers21,2262
Non-polymers942
Water1,856103
1
A: Carboxysome assembly protein CcmM
B: Carbonic anhydrase
hetero molecules

A: Carboxysome assembly protein CcmM
B: Carbonic anhydrase
hetero molecules

A: Carboxysome assembly protein CcmM
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,96012
Polymers63,6786
Non-polymers2826
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8330 Å2
ΔGint-59 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.365, 89.365, 129.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-202-

CL

21A-382-

HOH

31A-390-

HOH

41A-392-

HOH

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Components

#1: Protein Carboxysome assembly protein CcmM / CcmM58 / M58 / Carbon dioxide concentrating mechanism protein CcmM / Carboxysome shell associated protein CcmM


Mass: 19249.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: ccmM, Synpcc7942_1423 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03513
#2: Protein/peptide Carbonic anhydrase / / Carbonate dehydratase


Mass: 1976.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Strain: PCC 7942 / FACHB-805 / Gene: ccaA, icfA, Synpcc7942_1447 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27134, carbonic anhydrase
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG-3350 and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99989 Å / Relative weight: 1
ReflectionResolution: 1.63→37.08 Å / Num. obs: 24740 / % possible obs: 98.8 % / Redundancy: 18.4 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.031 / Net I/σ(I): 45.4
Reflection shellResolution: 1.632→1.661 Å / Rmerge(I) obs: 0.684 / Num. unique obs: 1128 / CC1/2: 0.865 / Rrim(I) all: 0.725

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O4Z

7o4z


Resolution: 1.63→37.08 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.417 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1186 4.8 %RANDOM
Rwork0.1773 ---
obs0.1785 23554 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.71 Å2 / Biso mean: 34.751 Å2 / Biso min: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å20 Å2
2---0.03 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.63→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 2 103 1481
Biso mean--38.24 43.84 -
Num. residues----180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131405
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171338
X-RAY DIFFRACTIONr_angle_refined_deg2.0991.6351909
X-RAY DIFFRACTIONr_angle_other_deg1.4951.5793056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.37520.85482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94715214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5851514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
LS refinement shellResolution: 1.632→1.675 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 89 -
Rwork0.284 1584 -
all-1673 -
obs--91.37 %
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)
10.8130.4043-0.07230.27880.17080.75350.02060.0498-0.12440.00330.0253-0.02810.00690.0335-0.04590.01670.0018-0.02670.0209-0.03160.1423-3.3779-15.4233-20.9157
23.2605-0.12622.78612.81441.743.59610.4437-0.0208-0.7521-0.12890.4845-0.40590.30710.3023-0.92820.0726-0.0035-0.05980.13-0.00710.32729.41-23.5664-10.9447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 180
2X-RAY DIFFRACTION2B256 - 270

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