5DQL
Crystal Structure of 2-vinyl glyoxylate modified isocitrate lyase from Mycobacterium tuberculosis
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004451 | molecular_function | isocitrate lyase activity |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006097 | biological_process | glyoxylate cycle |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0006102 | biological_process | isocitrate metabolic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0035375 | molecular_function | zymogen binding |
| A | 0046421 | molecular_function | methylisocitrate lyase activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0071456 | biological_process | cellular response to hypoxia |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004451 | molecular_function | isocitrate lyase activity |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006097 | biological_process | glyoxylate cycle |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0006102 | biological_process | isocitrate metabolic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0035375 | molecular_function | zymogen binding |
| B | 0046421 | molecular_function | methylisocitrate lyase activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0071456 | biological_process | cellular response to hypoxia |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004451 | molecular_function | isocitrate lyase activity |
| C | 0005576 | cellular_component | extracellular region |
| C | 0005829 | cellular_component | cytosol |
| C | 0005886 | cellular_component | plasma membrane |
| C | 0006097 | biological_process | glyoxylate cycle |
| C | 0006099 | biological_process | tricarboxylic acid cycle |
| C | 0006102 | biological_process | isocitrate metabolic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0019752 | biological_process | carboxylic acid metabolic process |
| C | 0035375 | molecular_function | zymogen binding |
| C | 0046421 | molecular_function | methylisocitrate lyase activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0071456 | biological_process | cellular response to hypoxia |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004451 | molecular_function | isocitrate lyase activity |
| D | 0005576 | cellular_component | extracellular region |
| D | 0005829 | cellular_component | cytosol |
| D | 0005886 | cellular_component | plasma membrane |
| D | 0006097 | biological_process | glyoxylate cycle |
| D | 0006099 | biological_process | tricarboxylic acid cycle |
| D | 0006102 | biological_process | isocitrate metabolic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0019752 | biological_process | carboxylic acid metabolic process |
| D | 0035375 | molecular_function | zymogen binding |
| D | 0046421 | molecular_function | methylisocitrate lyase activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0071456 | biological_process | cellular response to hypoxia |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 501 |
| Chain | Residue |
| A | ASP153 |
| A | HOH604 |
| A | HOH647 |
| A | HOH787 |
| A | HOH879 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 502 |
| Chain | Residue |
| A | HOH669 |
| A | HOH869 |
| A | ALA276 |
| A | ALA279 |
| A | GLN308 |
| A | HOH666 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | binding site for residue VGX A 503 |
| Chain | Residue |
| A | TRP93 |
| A | ASP108 |
| A | CYS191 |
| A | GLY192 |
| A | HIS193 |
| A | ASN313 |
| A | SER315 |
| A | SER317 |
| A | THR347 |
| A | LEU348 |
| A | HOH603 |
| A | HOH787 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue MG B 501 |
| Chain | Residue |
| B | ASP108 |
| B | ASP153 |
| B | HOH637 |
| B | HOH674 |
| B | HOH694 |
| B | HOH699 |
| B | HOH855 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue MG C 501 |
| Chain | Residue |
| C | ASP108 |
| C | ASP153 |
| C | HOH616 |
| C | HOH696 |
| C | HOH698 |
| C | HOH766 |
| C | HOH821 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue MG D 501 |
| Chain | Residue |
| D | TRP93 |
| D | ASP108 |
| D | ASP153 |
| D | HOH602 |
| D | HOH659 |
| D | HOH666 |
| D | HOH724 |
| D | HOH818 |
| site_id | AC7 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide VGX B 502 and CYS B 191 |
| Chain | Residue |
| A | GLN394 |
| B | TRP93 |
| B | ASP108 |
| B | LYS190 |
| B | GLY192 |
| B | HIS193 |
| B | LEU194 |
| B | ASN313 |
| B | SER315 |
| B | SER317 |
| B | THR347 |
| B | LEU348 |
| B | HOH641 |
| B | HOH694 |
| site_id | AC8 |
| Number of Residues | 13 |
| Details | binding site for Di-peptide VGX C 502 and CYS C 191 |
| Chain | Residue |
| C | TRP93 |
| C | ASP108 |
| C | LYS190 |
| C | GLY192 |
| C | HIS193 |
| C | LEU194 |
| C | ASN313 |
| C | SER315 |
| C | SER317 |
| C | THR347 |
| C | LEU348 |
| C | HOH605 |
| D | GLN394 |
| site_id | AC9 |
| Number of Residues | 11 |
| Details | binding site for Di-peptide VGX D 502 and CYS D 191 |
| Chain | Residue |
| C | GLN394 |
| D | TRP93 |
| D | ASP108 |
| D | LYS190 |
| D | GLY192 |
| D | HIS193 |
| D | LEU194 |
| D | ASN313 |
| D | SER315 |
| D | SER317 |
| D | THR347 |
Functional Information from PROSITE/UniProt
| site_id | PS00161 |
| Number of Residues | 6 |
| Details | ISOCITRATE_LYASE Isocitrate lyase signature. KKCGHL |
| Chain | Residue | Details |
| A | LYS189-LEU194 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"24354272","evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 40 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10932251","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | Cross-link: {"description":"Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)","evidences":[{"source":"PubMed","id":"20066036","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| A | ASP153 | metal ligand |
| A | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| A | CYS191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| A | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| A | ARG228 | electrostatic stabiliser, hydrogen bond donor |
| A | SER315 | electrostatic stabiliser, hydrogen bond donor |
| A | SER317 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| B | ASP153 | metal ligand |
| B | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| B | CYS191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| B | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| B | ARG228 | electrostatic stabiliser, hydrogen bond donor |
| B | SER315 | electrostatic stabiliser, hydrogen bond donor |
| B | SER317 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA3 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| C | ASP153 | metal ligand |
| C | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| C | CYS191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| C | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| C | ARG228 | electrostatic stabiliser, hydrogen bond donor |
| C | SER315 | electrostatic stabiliser, hydrogen bond donor |
| C | SER317 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA4 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| D | ASP153 | metal ligand |
| D | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| D | CYS191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| D | HIS193 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| D | ARG228 | electrostatic stabiliser, hydrogen bond donor |
| D | SER315 | electrostatic stabiliser, hydrogen bond donor |
| D | SER317 | electrostatic stabiliser, hydrogen bond donor |
