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- EMDB-32775: Cryo-EM structure of human pyruvate carboxylase with acetyl-CoA -

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Basic information

Entry
Database: EMDB / ID: EMD-32775
TitleCryo-EM structure of human pyruvate carboxylase with acetyl-CoA
Map data
Sample
  • Complex: PC
    • Protein or peptide: Pyruvate carboxylase, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: ACETYL COENZYME *A
Function / homology
Function and homology information


pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / viral RNA genome packaging / NADP metabolic process / Pyruvate metabolism / positive regulation by host of viral process / Gluconeogenesis / NADH metabolic process ...pyruvate carboxylase / pyruvate carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / viral RNA genome packaging / NADP metabolic process / Pyruvate metabolism / positive regulation by host of viral process / Gluconeogenesis / NADH metabolic process / pyruvate metabolic process / biotin binding / viral release from host cell / gluconeogenesis / lipid metabolic process / mitochondrial matrix / negative regulation of gene expression / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal ...Pyruvate carboxylase / Carboxylase, conserved domain / Conserved carboxylase domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyruvate carboxylase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChai P / Lan P / Wu J / Lei M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Cell / Year: 2022
Title: Mechanistic insight into allosteric activation of human pyruvate carboxylase by acetyl-CoA.
Authors: Peiwei Chai / Pengfei Lan / Shaobai Li / Deqiang Yao / Chenchen Chang / Mi Cao / Yafeng Shen / Shengfang Ge / Jian Wu / Ming Lei / Xianqun Fan /
Abstract: Pyruvate carboxylase (PC) catalyzes the two-step carboxylation of pyruvate to produce oxaloacetate, playing a key role in the maintenance of metabolic homeostasis in cells. Given its involvement in ...Pyruvate carboxylase (PC) catalyzes the two-step carboxylation of pyruvate to produce oxaloacetate, playing a key role in the maintenance of metabolic homeostasis in cells. Given its involvement in multiple diseases, PC has been regarded as a potential therapeutic target for obesity, diabetes, and cancer. Albeit acetyl-CoA has been recognized as the allosteric regulator of PC for over 60 years, the underlying mechanism of how acetyl-CoA induces PC activation remains enigmatic. Herein, by using time-resolved cryo-electron microscopy, we have captured the snapshots of PC transitional states during its catalytic cycle. These structures and the biochemical studies reveal that acetyl-CoA stabilizes PC in a catalytically competent conformation, which triggers a cascade of events, including ATP hydrolysis and the long-distance communication between the two reactive centers. These findings provide an integrated picture for PC catalysis and unveil the unique allosteric mechanism of acetyl-CoA in an essential biochemical reaction in all kingdoms of life.
History
DepositionFeb 4, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 16, 2022-
Current statusNov 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32775.png

Downloads & links

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Map

FileDownload / File: emd_32775.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 312 pix.
= 343.2 Å		1.1 Å/pix.
x 312 pix.
= 343.2 Å		1.1 Å/pix.
x 312 pix.
= 343.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.017063154 - 0.04380833
Average (Standard dev.)0.00016773434 (±0.0015403352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 343.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_32775_additional_1.map
Projections & Slices
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Additional map: #2

Fileemd_32775_additional_2.map
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Additional map: #3

Fileemd_32775_additional_3.map
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Sample components

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Entire : PC

EntireName: PC
Components
  • Complex: PC
    • Protein or peptide: Pyruvate carboxylase, mitochondrial
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: PC

SupramoleculeName: PC / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pyruvate carboxylase, mitochondrial

MacromoleculeName: Pyruvate carboxylase, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: pyruvate carboxylase
Source (natural)Organism: human (human)
Molecular weightTheoretical: 129.799359 KDa
SequenceString: MLKFRTVHGG LRLLGIRRTS TAPAASPNVR RLEYKPIKKV MVANRGEIAI RVFRACTELG IRTVAIYSEQ DTGQMHRQKA DEAYLIGRG LAPVQAYLHI PDIIKVAKEN NVDAVHPGYG FLSERADFAQ ACQDAGVRFI GPSPEVVRKM GDKVEARAIA I AAGVPVVP ...String:
MLKFRTVHGG LRLLGIRRTS TAPAASPNVR RLEYKPIKKV MVANRGEIAI RVFRACTELG IRTVAIYSEQ DTGQMHRQKA DEAYLIGRG LAPVQAYLHI PDIIKVAKEN NVDAVHPGYG FLSERADFAQ ACQDAGVRFI GPSPEVVRKM GDKVEARAIA I AAGVPVVP GTDAPITSLH EAHEFSNTYG FPIIFKAAYG GGGRGMRVVH SYEELEENYT RAYSEALAAF GNGALFVEKF IE KPRHIEV QILGDQYGNI LHLYERDCSI QRRHQKVVEI APAAHLDPQL RTRLTSDSVK LAKQVGYENA GTVEFLVDRH GKH YFIEVN SRLQVEHTVT EEITDVDLVH AQIHVAEGRS LPDLGLRQEN IRINGCAIQC RVTTEDPARS FQPDTGRIEV FRSG EGMGI RLDNASAFQG AVISPHYDSL LVKVIAHGKD HPTAATKMSR ALAEFRVRGV KTNIAFLQNV LNNQQFLAGT VDTQF IDEN PELFQLRPAQ NRAQKLLHYL GHVMVNGPTT PIPVKASPSP TDPVVPAVPI GPPPAGFRDI LLREGPEGFA RAVRNH PGL LLMDTTFRDA HQSLLATRVR THDLKKIAPY VAHNFSKLFS MENWGGATFD VAMRFLYECP WRRLQELREL IPNIPFQ ML LRGANAVGYT NYPDNVVFKF CEVAKENGMD VFRVFDSLNY LPNMLLGMEA AGSAGGVVEA AISYTGDVAD PSRTKYSL Q YYMGLAEELV RAGTHILCIK DMAGLLKPTA CTMLVSSLRD RFPDLPLHIH THDTSGAGVA AMLACAQAGA DVVDVAADS MSGMTSQPSM GALVACTRGT PLDTEVPMER VFDYSEYWEG ARGLYAAFDC TATMKSGNSD VYENEIPGGQ YTNLHFQAHS MGLGSKFKE VKKAYVEANQ MLGDLIKVTP SSKIVGDLAQ FMVQNGLSRA EAEAQAEELS FPRSVVEFLQ GYIGVPHGGF P EPFRSKVL KDLPRVEGRP GASLPPLDLQ ALEKELVDRH GEEVTPEDVL SAAMYPDVFA HFKDFTATFG PLDSLNTRLF LQ GPKIAEE FEVELERGKT LHIKALAVSD LNRAGQRQVF FELNGQLRSI LVKDTQAMKE MHFHPKALKD VKGQIGAPMP GKV IDIKVV AGAKVAKGQP LCVLSAMKME TVVTSPMEGT VRKVHVTKDM TLEGDDLILE IE

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Macromolecule #2: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

MacromoleculeName: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
type: ligand / ID: 2 / Number of copies: 4 / Formula: BTI
Molecular weightTheoretical: 228.311 Da
Chemical component information

ChemComp-BTI:
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 4 / Number of copies: 2 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3bg5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186526
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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