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- PDB-9uhb: BCCP-CT Conformation of AMPPNP-bound hPCC -

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Basic information

Entry
Database: PDB / ID: 9uhb
TitleBCCP-CT Conformation of AMPPNP-bound hPCC
Components
  • (Propionyl-CoA carboxylase beta chain, ...) x 2
  • Propionyl-CoA carboxylase alpha chain, mitochondrial
KeywordsTRANSFERASE / carboxylase
Function / homology
Function and homology information


short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation ...short-chain fatty acid catabolic process / branched-chain amino acid metabolic process / Propionyl-CoA catabolism / propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / biotin binding / catalytic complex / Mitochondrial protein degradation / fatty acid metabolic process / mitochondrial matrix / enzyme binding / mitochondrion / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase 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 synthase subdomain signature 1. / 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 / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
propionyl Coenzyme A / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / BIOTIN / Propionyl-CoA carboxylase alpha chain, mitochondrial / Propionyl-CoA carboxylase beta chain, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsNi, F.Y. / Yan, H.F. / Wang, Q.H. / Ma, J.P.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2021YFF1200400 China
Other government2018SHZDZX01 China
CitationJournal: Structure / Year: 2025
Title: Nanoscale conformational dynamics of human propionyl-CoA carboxylase.
Authors: Huifang Yan / Fengyun Ni / Qinghua Wang / Jianpeng Ma /
Abstract: Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic ...Propionyl-CoA carboxylase (PCC) is a biotin-dependent mitochondrial enzyme responsible for propionyl-CoA catabolism. Deficiencies in human PCC (hPCC) cause propionic acidemia, a severe metabolic disorder driven by toxic metabolite accumulation. Despite its therapeutic relevance, the structural basis of hPCC's catalytic function remains unresolved. Here, we present high-resolution cryo-EM structures of hPCC in four distinct states, unliganded, ADP-, AMPPNP-, and ATP-bound/substrate-bound, capturing the full trajectory of the biotin carboxyl carrier protein (BCCP) domain as it translocates between active sites. Our results reinforce the crucial role of nucleotide-gated B-lid subdomain in synchronizing catalysis through coupling with BCCP movement. Structural and biochemical analysis of 10 disease-associated variants reveals how mutations disrupt key domain interfaces and dynamic motions required for activity. These new insights define the mechanistic principles governing hPCC functions, establish a structural framework for understanding PCC-related disorders, and lay the groundwork for future efforts to engineer functional replacements or modulators for metabolic therapy.
History
DepositionApr 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Propionyl-CoA carboxylase alpha chain, mitochondrial
B: Propionyl-CoA carboxylase beta chain, mitochondrial
F: Propionyl-CoA carboxylase beta chain, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,0637
Polymers138,4653
Non-polymers1,5984
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Propionyl-CoA carboxylase alpha chain, mitochondrial / PCCase subunit alpha / Propanoyl-CoA:carbon dioxide ligase subunit alpha


Mass: 80161.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCA / Production host: Homo sapiens (human) / References: UniProt: P05165, propionyl-CoA carboxylase

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Propionyl-CoA carboxylase beta chain, ... , 2 types, 2 molecules BF

#2: Protein Propionyl-CoA carboxylase beta chain, mitochondrial / PCCase subunit beta / Propanoyl-CoA:carbon dioxide ligase subunit beta


Mass: 27095.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCB / Production host: Homo sapiens (human) / References: UniProt: P05166, propionyl-CoA carboxylase
#3: Protein Propionyl-CoA carboxylase beta chain, mitochondrial / PCCase subunit beta / Propanoyl-CoA:carbon dioxide ligase subunit beta


Mass: 31207.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCCB / Production host: Homo sapiens (human) / References: UniProt: P05166, propionyl-CoA carboxylase

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Non-polymers , 4 types, 4 molecules

#4: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Propionyl-CoA carboxylase / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101175 / Symmetry type: POINT
RefinementHighest resolution: 3.16 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029336
ELECTRON MICROSCOPYf_angle_d0.52212642
ELECTRON MICROSCOPYf_dihedral_angle_d9.3481326
ELECTRON MICROSCOPYf_chiral_restr0.0431428
ELECTRON MICROSCOPYf_plane_restr0.0041639

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