6C4C
Crystal structure of 3-nitropropionate modified isocitrate lyase from Mycobacterium tuberculosis with glyoxylate and pyruvate
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 |
| E | 0003824 | molecular_function | catalytic activity |
| E | 0004451 | molecular_function | isocitrate lyase activity |
| E | 0005576 | cellular_component | extracellular region |
| E | 0005829 | cellular_component | cytosol |
| E | 0005886 | cellular_component | plasma membrane |
| E | 0006097 | biological_process | glyoxylate cycle |
| E | 0006099 | biological_process | tricarboxylic acid cycle |
| E | 0006102 | biological_process | isocitrate metabolic process |
| E | 0016829 | molecular_function | lyase activity |
| E | 0019752 | biological_process | carboxylic acid metabolic process |
| E | 0035375 | molecular_function | zymogen binding |
| E | 0046421 | molecular_function | methylisocitrate lyase activity |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0071456 | biological_process | cellular response to hypoxia |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0004451 | molecular_function | isocitrate lyase activity |
| F | 0005576 | cellular_component | extracellular region |
| F | 0005829 | cellular_component | cytosol |
| F | 0005886 | cellular_component | plasma membrane |
| F | 0006097 | biological_process | glyoxylate cycle |
| F | 0006099 | biological_process | tricarboxylic acid cycle |
| F | 0006102 | biological_process | isocitrate metabolic process |
| F | 0016829 | molecular_function | lyase activity |
| F | 0019752 | biological_process | carboxylic acid metabolic process |
| F | 0035375 | molecular_function | zymogen binding |
| F | 0046421 | molecular_function | methylisocitrate lyase activity |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0071456 | biological_process | cellular response to hypoxia |
| G | 0003824 | molecular_function | catalytic activity |
| G | 0004451 | molecular_function | isocitrate lyase activity |
| G | 0005576 | cellular_component | extracellular region |
| G | 0005829 | cellular_component | cytosol |
| G | 0005886 | cellular_component | plasma membrane |
| G | 0006097 | biological_process | glyoxylate cycle |
| G | 0006099 | biological_process | tricarboxylic acid cycle |
| G | 0006102 | biological_process | isocitrate metabolic process |
| G | 0016829 | molecular_function | lyase activity |
| G | 0019752 | biological_process | carboxylic acid metabolic process |
| G | 0035375 | molecular_function | zymogen binding |
| G | 0046421 | molecular_function | methylisocitrate lyase activity |
| G | 0046872 | molecular_function | metal ion binding |
| G | 0071456 | biological_process | cellular response to hypoxia |
| H | 0003824 | molecular_function | catalytic activity |
| H | 0004451 | molecular_function | isocitrate lyase activity |
| H | 0005576 | cellular_component | extracellular region |
| H | 0005829 | cellular_component | cytosol |
| H | 0005886 | cellular_component | plasma membrane |
| H | 0006097 | biological_process | glyoxylate cycle |
| H | 0006099 | biological_process | tricarboxylic acid cycle |
| H | 0006102 | biological_process | isocitrate metabolic process |
| H | 0016829 | molecular_function | lyase activity |
| H | 0019752 | biological_process | carboxylic acid metabolic process |
| H | 0035375 | molecular_function | zymogen binding |
| H | 0046421 | molecular_function | methylisocitrate lyase activity |
| H | 0046872 | molecular_function | metal ion binding |
| H | 0071456 | biological_process | cellular response to hypoxia |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | binding site for residue GLV A 501 |
| Chain | Residue |
| A | TYR89 |
| A | THR347 |
| A | MG502 |
| A | SER91 |
| A | GLY92 |
| A | TRP93 |
| A | ASP153 |
| A | HIS180 |
| A | EJA191 |
| A | ARG228 |
| A | TRP283 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 502 |
| Chain | Residue |
| A | ASP108 |
| A | ASP153 |
| A | GLV501 |
| A | HOH603 |
| A | HOH610 |
| A | HOH653 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 503 |
| Chain | Residue |
| A | ALA276 |
| A | ALA279 |
| A | GLN308 |
| A | HOH666 |
| A | HOH797 |
| A | HOH816 |
| site_id | AC4 |
| Number of Residues | 15 |
| Details | binding site for residue PYR B 501 |
| Chain | Residue |
| B | TYR89 |
| B | SER91 |
| B | GLY92 |
| B | TRP93 |
| B | ASP108 |
| B | ASP153 |
| B | HIS180 |
| B | EJA191 |
| B | ARG228 |
| B | TRP283 |
| B | THR347 |
| B | MG502 |
| B | HOH604 |
| B | HOH613 |
| B | HOH661 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 502 |
| Chain | Residue |
| B | ASP108 |
| B | ASP153 |
| B | PYR501 |
| B | HOH604 |
| B | HOH613 |
| B | HOH661 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 503 |
| Chain | Residue |
| B | ALA276 |
| B | ALA279 |
| B | GLN308 |
| B | HOH659 |
| B | HOH771 |
| B | HOH773 |
| site_id | AC7 |
| Number of Residues | 14 |
| Details | binding site for residue PYR C 501 |
| Chain | Residue |
| C | TYR89 |
| C | SER91 |
| C | GLY92 |
| C | TRP93 |
| C | ASP153 |
| C | HIS180 |
| C | EJA191 |
| C | ARG228 |
| C | TRP283 |
| C | THR347 |
| C | MG502 |
| C | HOH604 |
| C | HOH619 |
| C | HOH636 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 502 |
| Chain | Residue |
| C | ASP153 |
| C | PYR501 |
| C | HOH604 |
| C | HOH619 |
| C | HOH636 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 503 |
| Chain | Residue |
| C | ALA276 |
| C | ALA279 |
| C | GLN308 |
| C | HOH637 |
| C | HOH766 |
| C | HOH770 |
| site_id | AD1 |
| Number of Residues | 12 |
| Details | binding site for residue GLV D 501 |
| Chain | Residue |
| D | TYR89 |
| D | SER91 |
| D | GLY92 |
| D | TRP93 |
| D | ASP153 |
| D | HIS180 |
| D | EJA191 |
| D | ARG228 |
| D | THR347 |
| D | MG502 |
| D | HOH601 |
| D | HOH628 |
| site_id | AD2 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 502 |
| Chain | Residue |
| D | ASP108 |
| D | ASP153 |
| D | GLV501 |
| D | HOH601 |
| D | HOH628 |
| D | HOH641 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 503 |
| Chain | Residue |
| D | ALA276 |
| D | ALA279 |
| D | GLN308 |
| D | HOH617 |
| D | HOH765 |
| D | HOH769 |
| site_id | AD4 |
| Number of Residues | 14 |
| Details | binding site for residue PYR E 501 |
| Chain | Residue |
| E | TYR89 |
| E | SER91 |
| E | GLY92 |
| E | TRP93 |
| E | ASP108 |
| E | ASP153 |
| E | EJA191 |
| E | ARG228 |
| E | TRP283 |
| E | THR347 |
| E | MG502 |
| E | HOH604 |
| E | HOH612 |
| E | HOH658 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue MG E 502 |
| Chain | Residue |
| E | ASP108 |
| E | ASP153 |
| E | PYR501 |
| E | HOH604 |
| E | HOH612 |
| E | HOH658 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue MG E 503 |
| Chain | Residue |
| E | ALA276 |
| E | ALA279 |
| E | GLN308 |
| E | HOH602 |
| E | HOH769 |
| E | HOH788 |
| site_id | AD7 |
| Number of Residues | 10 |
| Details | binding site for residue 3NP E 504 |
| Chain | Residue |
| E | TYR356 |
| E | SER357 |
| E | LEU376 |
| E | ARG379 |
| E | HOH601 |
| E | HOH605 |
| E | HOH757 |
| F | TYR356 |
| F | SER357 |
| F | ARG379 |
| site_id | AD8 |
| Number of Residues | 12 |
| Details | binding site for residue PYR F 501 |
| Chain | Residue |
| F | TYR89 |
| F | SER91 |
| F | GLY92 |
| F | TRP93 |
| F | ASP153 |
| F | EJA191 |
| F | ARG228 |
| F | TRP283 |
| F | THR347 |
| F | MG502 |
| F | HOH608 |
| F | HOH661 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue MG F 502 |
| Chain | Residue |
| F | ASP108 |
| F | ASP153 |
| F | PYR501 |
| F | HOH608 |
| F | HOH617 |
| F | HOH661 |
| site_id | AE1 |
| Number of Residues | 14 |
| Details | binding site for residue PYR G 501 |
| Chain | Residue |
| G | TYR89 |
| G | SER91 |
| G | GLY92 |
| G | TRP93 |
| G | ASP108 |
| G | ASP153 |
| G | EJA191 |
| G | ARG228 |
| G | TRP283 |
| G | THR347 |
| G | MG502 |
| G | HOH606 |
| G | HOH614 |
| G | HOH650 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue MG G 502 |
| Chain | Residue |
| G | ASP108 |
| G | ASP153 |
| G | PYR501 |
| G | HOH606 |
| G | HOH614 |
| G | HOH650 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue MG G 503 |
| Chain | Residue |
| G | ALA276 |
| G | ALA279 |
| G | GLN308 |
| G | HOH736 |
| G | HOH771 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue MG H 501 |
| Chain | Residue |
| E | HOH768 |
| H | ASP34 |
| H | HOH657 |
| H | HOH683 |
| H | HOH746 |
| site_id | AE5 |
| Number of Residues | 14 |
| Details | binding site for residue GLV H 502 |
| Chain | Residue |
| H | TYR89 |
| H | SER91 |
| H | GLY92 |
| H | TRP93 |
| H | ASP108 |
| H | ASP153 |
| H | HIS180 |
| H | EJA191 |
| H | ARG228 |
| H | THR347 |
| H | MG503 |
| H | HOH601 |
| H | HOH606 |
| H | HOH621 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue MG H 503 |
| Chain | Residue |
| H | ASP108 |
| H | ASP153 |
| H | GLV502 |
| H | HOH601 |
| H | HOH606 |
| H | HOH621 |
| site_id | AE7 |
| Number of Residues | 6 |
| Details | binding site for residue MG H 504 |
| Chain | Residue |
| H | ALA276 |
| H | ALA279 |
| H | GLN308 |
| H | HOH679 |
| H | HOH761 |
| H | HOH767 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| 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 | 80 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"10932251","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| 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 | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| A | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| A | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| A | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| A | LYS321 | 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 | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| B | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| B | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| B | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| B | LYS321 | 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 | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| C | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| C | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| C | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| C | LYS321 | 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 | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| D | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| D | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| D | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| D | LYS321 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA5 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| E | ASP153 | metal ligand |
| E | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| E | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| E | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| E | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| E | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| E | LYS321 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA6 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| F | ASP153 | metal ligand |
| F | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| F | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| F | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| F | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| F | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| F | LYS321 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA7 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| G | ASP153 | metal ligand |
| G | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| G | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| G | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| G | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| G | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| G | LYS321 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA8 |
| Number of Residues | 7 |
| Details | M-CSA 272 |
| Chain | Residue | Details |
| H | ASP153 | metal ligand |
| H | HIS180 | electrostatic stabiliser, hydrogen bond donor |
| H | EJA191 | covalent catalysis, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay, proton shuttle (general acid/base) |
| H | LYS197 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton shuttle (general acid/base) |
| H | GLU232 | electrostatic stabiliser, hydrogen bond donor |
| H | ASN319 | electrostatic stabiliser, hydrogen bond donor |
| H | LYS321 | electrostatic stabiliser, hydrogen bond donor |
