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- EMDB-15029: Cryo-EM structure of "CT oxa" conformation of Lactococcus lactis ... -
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Open data
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Basic information
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Title | Cryo-EM structure of "CT oxa" conformation of Lactococcus lactis pyruvate carboxylase with acetyl-CoA | |||||||||
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Function / homology | ![]() pyruvate carboxylase / pyruvate carboxylase activity / pyruvate metabolic process / gluconeogenesis / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.47 Å | |||||||||
![]() | Lopez-Alonso JP / Lazaro M / Gil D / Choi PH / Tong L / Valle M | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase. Authors: Jorge Pedro López-Alonso / Melisa Lázaro / David Gil-Cartón / Philip H Choi / Alexandra Dodu / Liang Tong / Mikel Valle / ![]() ![]() Abstract: Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both ...Pyruvate carboxylase (PC) is a tetrameric enzyme that contains two active sites per subunit that catalyze two consecutive reactions. A mobile domain with an attached prosthetic biotin links both reactions, an initial biotin carboxylation and the subsequent carboxyl transfer to pyruvate substrate to produce oxaloacetate. Reaction sites are at long distance, and there are several co-factors that play as allosteric regulators. Here, using cryoEM we explore the structure of active PC tetramers focusing on active sites and on the conformational space of the oligomers. The results capture the mobile domain at both active sites and expose catalytic steps of both reactions at high resolution, allowing the identification of substrates and products. The analysis of catalytically active PC tetramers reveals the role of certain motions during enzyme functioning, and the structural changes in the presence of additional cofactors expose the mechanism for allosteric regulation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 938.2 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.6 KB 21.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 116 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Others | ![]() ![]() | 80.9 MB 81 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zyzMC ![]() 7zyyC ![]() 7zz0C ![]() 7zz1C ![]() 7zz2C ![]() 7zz3C ![]() 7zz4C ![]() 7zz5C ![]() 7zz6C ![]() 7zz8C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Sample components
-Entire : Pyruvate carboxylase with acetyl coenzyme A
Entire | Name: Pyruvate carboxylase with acetyl coenzyme A |
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Components |
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-Supramolecule #1: Pyruvate carboxylase with acetyl coenzyme A
Supramolecule | Name: Pyruvate carboxylase with acetyl coenzyme A / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Pyruvate carboxylase
Macromolecule | Name: Pyruvate carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: pyruvate carboxylase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 127.349578 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VPRGSHMKKL LVANRGEIAV RVFRACNELG LSTVAVYARE DEYSVHRFKA DESYLIGQGK KPIDAYLDID DIIRVALESG ADAIHPGYG LLSENLEFAT KVRAAGLVFV GPELHHLDIF GDKIKAKAAA DEAKVPGIPG TNGAVDIDGA LEFAKTYGYP V MIKAALGG ...String: VPRGSHMKKL LVANRGEIAV RVFRACNELG LSTVAVYARE DEYSVHRFKA DESYLIGQGK KPIDAYLDID DIIRVALESG ADAIHPGYG LLSENLEFAT KVRAAGLVFV GPELHHLDIF GDKIKAKAAA DEAKVPGIPG TNGAVDIDGA LEFAKTYGYP V MIKAALGG GGRGMRVARN DAEMHDGYAR AKSEAIGAFG SGEIYVEKYI ENPKHIEVQI LGDRHGNIIH LHERDCSVQR RN QKVIEIA PAVGLSPDFR NEICEAAVKL CKNVGYVNAG TVEFLVKDDK FYFIEVNPRV QVEHTITELI TGVDIVQAQI LIA QGKDLH REIGLPAQSE IPLLGSAIQC RITTEDPQNG FLPDTGKIDT YRSPGGFGIR LDVGNAYAGY EVTPYFDSLL VKVC TFANE FSDSVRKMDR VLHEFRIRGV KTNIPFLINV IANENFTSGQ ATTTFIDNTP SLFNFPRLRD RGTKTLHYLS MITVN GFPG IENTEKRHFE EPRQPLLNLE KKKTAKNILD EQGADAVVDY VKNTKEVLLT DTTLRDAHQS LLATRLRLQD MKGIAQ AID QGLPELFSAE MWGGATFDVA YRFLNESPWY RLRKLRKLMP NTMFQMLFRG SNAVGYQNYP DNVIEEFIRV AAHEGID VF RIFDSLNWLP QMEKSIQAVR DNGKIAEATI CYTGDILDPS RPKYNIQYYK DLAKELEATG AHILAV(KCX)DMA GLLK PQAAY RLISELKDTV DLPIHLHTHD TSGNGIITYS GATQAGVDII DVATASLAGG TSQPSMQSIY YALEHGPRHA SINVK NAEQ IDHYWEDVRK YYAPFEAGIT SPQTEVYMHE MPGGQYTNLK SQAAAVGLGH RFDEIKQMYR KVNMMFGDII KVTPSS KVV GDMALFMIQN DLTEEDVYAR GNELNFPESV VSFFRGDLGQ PVGGFPEKLQ KIIVKDKAVI TDRPGLHAEK VDFETVK AD LEQKIGYEPG DHEVISYIMY PQVFLDYQKM QREFGAVTLL DTPTFLHGMR LNEKIEVQIE KGKTLSIRLD EIGEPDLA G NRVLFFNLNG QRREVVINDQ SVQAQVVAKR KAETGNPNQI GATMPGSVLE ILVKAGDKVQ KGQALMVTEA MKMETTIEA PFDGEIVDLH VVKGEAIQTQ DLLIEIN |
-Macromolecule #2: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Macromolecule #3: OXALOACETATE ION
Macromolecule | Name: OXALOACETATE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: OAA |
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Molecular weight | Theoretical: 131.064 Da |
Chemical component information | ![]() ChemComp-OAA: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 38 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 3D array |
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Sample preparation
Concentration | 0.05 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10518 / Average exposure time: 3.99 sec. / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |