Protein profile

VK055_2539

citrate (pro-3S)-lyase, beta subunit

Genome: KpATCC43816

Gene: citE AIK81136.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRI7
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Amino acids 283
Annotations 5
Features 13
PDB binders 4
Druggability 0.506

Overview

Basic information about this protein and its source genome.

Accession
VK055_2539
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
citE AIK81136.1
Status
annotated
Amino acids
283
Structure source
AlphaFold + ColabFold
GO
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0009346 Citrate lyase is a multienzyme complex with three constituents: the alpha subunit, citrate-ACP transferase; the beta subunit, citryl-ACP lyase; and the gamma subunit, an acyl-carrier protein which also carries the prosthetic group components. All three subunits are required for citrate lyase enzyme activity. This enzyme has only been found in bacteria. GO:0006084 The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis. GO:0008816 Catalysis of the reaction: (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.313
Human E-value
1.87e-14
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
64.211
DEG E-value
9.31e-125
Localization
Cytoplasmic
ColabFold pLDDT
95.99

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.506
Structure A0A0H3GRI7
Pocket Pocket 16
P2Rank 0.608
Structure A0A0H3GRI7
Pocket Pocket 1
ColabFold model
FPocket 0.6 · Pocket 3
P2Rank 0.587 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 235 / 4744 genomes with a hit
Normalized 0.05

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0009346 Citrate lyase is a multienzyme complex with three constituents: the alpha subunit, citrate-ACP transferase; the beta subunit, citryl-ACP lyase; and the gamma subunit, an acyl-carrier protein which also carries the prosthetic group components. All three subunits are required for citrate lyase enzyme activity. This enzyme has only been found in bacteria.
  • GO:0006084 The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis.
  • GO:0008816 Catalysis of the reaction: (3S)-citryl-CoA = acetyl-CoA + oxaloacetate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 281 FunFam G3DSA:3.20.20.60:FF:000008 Citrate (Pro-3S)-lyase subunit beta
1 217 Pfam PF03328 HpcH/HpaI aldolase/citrate lyase family
1 217 InterPro IPR005000 HpcH/HpaI aldolase/citrate lyase domain
1 227 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
1 227 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
88 108 Coils Coil Coil
1 280 Gene3D G3DSA:3.20.20.60 -
1 280 InterPro IPR040442 Pyruvate kinase-like domain superfamily
1 277 PANTHER PTHR32308 LYASE BETA SUBUNIT, PUTATIVE (AFU_ORTHOLOGUE AFUA_4G13030)-RELATED
1 283 PIRSF PIRSF015582 Cit_lyase_B
1 283 InterPro IPR011206 Citrate lyase beta subunit-like
1 281 NCBIfam TIGR01588 citrate (pro-3S)-lyase subunit beta
1 281 InterPro IPR006475 Citrate lyase, beta subunit, bacteria

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GRI7
AlphaFold — — full sequence — Viewing
ColabFold VK055_2539
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
16 0.506
3 0.301
10 0.0

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 13.57 0.608
2 3.92 0.125
3 2.07 0.039

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

36 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1VU
4L9Y
Q3J5L6 823.6 Da LogP -0.93 TPSA 363.6 3 viol. ✓ Clean CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O…
GLV
4L9Y
Q3J5L6 74.0 Da LogP -0.73 TPSA 54.4 ✓ Ro5 ✓ Clean C(=O)C(=O)O
OAA
1SGJ
Q9RUZ0 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
OXL
6KKH
A7NHT0 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.