2A5H
2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003824 | molecular_function | catalytic activity |
A | 0016853 | molecular_function | isomerase activity |
A | 0019475 | biological_process | L-lysine catabolic process to acetate |
A | 0046872 | molecular_function | metal ion binding |
A | 0050066 | molecular_function | L-lysine 2,3-aminomutase activity |
A | 0051536 | molecular_function | iron-sulfur cluster binding |
A | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
B | 0003824 | molecular_function | catalytic activity |
B | 0016853 | molecular_function | isomerase activity |
B | 0019475 | biological_process | L-lysine catabolic process to acetate |
B | 0046872 | molecular_function | metal ion binding |
B | 0050066 | molecular_function | L-lysine 2,3-aminomutase activity |
B | 0051536 | molecular_function | iron-sulfur cluster binding |
B | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
C | 0003824 | molecular_function | catalytic activity |
C | 0016853 | molecular_function | isomerase activity |
C | 0019475 | biological_process | L-lysine catabolic process to acetate |
C | 0046872 | molecular_function | metal ion binding |
C | 0050066 | molecular_function | L-lysine 2,3-aminomutase activity |
C | 0051536 | molecular_function | iron-sulfur cluster binding |
C | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
D | 0003824 | molecular_function | catalytic activity |
D | 0016853 | molecular_function | isomerase activity |
D | 0019475 | biological_process | L-lysine catabolic process to acetate |
D | 0046872 | molecular_function | metal ion binding |
D | 0050066 | molecular_function | L-lysine 2,3-aminomutase activity |
D | 0051536 | molecular_function | iron-sulfur cluster binding |
D | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE ZN A 421 |
Chain | Residue |
A | CYS268 |
B | CYS375 |
B | CYS377 |
B | CYS380 |
site_id | AC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 A 592 |
Chain | Residue |
A | HIS111 |
A | TYR113 |
D | ARG409 |
site_id | AC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE ZN B 421 |
Chain | Residue |
A | CYS380 |
B | CYS268 |
A | CYS375 |
A | CYS377 |
site_id | AC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 C 593 |
Chain | Residue |
B | ARG409 |
C | HIS111 |
C | ARG112 |
C | TYR113 |
site_id | AC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE ZN C 421 |
Chain | Residue |
C | CYS268 |
D | CYS375 |
D | CYS377 |
D | CYS380 |
site_id | AC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 D 494 |
Chain | Residue |
A | ARG409 |
D | HIS111 |
D | ARG112 |
D | TYR113 |
site_id | AC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE ZN D 421 |
Chain | Residue |
C | CYS375 |
C | CYS377 |
C | CYS380 |
D | CYS268 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 B 495 |
Chain | Residue |
B | HIS111 |
B | ARG112 |
B | TYR113 |
C | ARG409 |
site_id | AC9 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE SAM A 417 |
Chain | Residue |
A | HIS131 |
A | THR133 |
A | ARG134 |
A | SER169 |
A | GLY171 |
A | HIS230 |
A | GLN258 |
A | VAL260 |
A | TYR290 |
A | GLN291 |
A | CYS292 |
A | ASP293 |
A | LEU298 |
A | SF4418 |
A | LYS420 |
A | HOH603 |
site_id | BC1 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE SAM B 417 |
Chain | Residue |
B | HIS131 |
B | THR133 |
B | ARG134 |
B | SER169 |
B | GLY171 |
B | GLY200 |
B | HIS230 |
B | GLN258 |
B | VAL260 |
B | TYR290 |
B | GLN291 |
B | CYS292 |
B | ASP293 |
B | LEU298 |
B | SF4418 |
B | LYS420 |
B | HOH524 |
site_id | BC2 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE SAM C 417 |
Chain | Residue |
C | HIS131 |
C | THR133 |
C | ARG134 |
C | SER169 |
C | GLY171 |
C | HIS230 |
C | GLN258 |
C | VAL260 |
C | TYR290 |
C | GLN291 |
C | CYS292 |
C | ASP293 |
C | LEU298 |
C | SF4418 |
C | LYS420 |
C | HOH627 |
site_id | BC3 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE SAM D 417 |
Chain | Residue |
D | HIS131 |
D | THR133 |
D | ARG134 |
D | SER169 |
D | GLY171 |
D | HIS230 |
D | GLN258 |
D | VAL260 |
D | TYR290 |
D | GLN291 |
D | CYS292 |
D | ASP293 |
D | LEU298 |
D | SF4418 |
D | LYS420 |
D | HOH533 |
site_id | BC4 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE LYS A 420 |
Chain | Residue |
A | SER169 |
A | TYR290 |
A | ASP293 |
A | ASP330 |
A | SAM417 |
A | PLP419 |
A | HOH625 |
A | LEU118 |
A | ARG134 |
A | LEU167 |
site_id | BC5 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP A 419 |
Chain | Residue |
A | THR110 |
A | TYR113 |
A | ARG116 |
A | LEU118 |
A | ARG198 |
A | TYR287 |
A | TYR288 |
A | LYS337 |
A | LYS420 |
A | HOH596 |
A | HOH600 |
A | HOH612 |
A | HOH724 |
B | SER320 |
B | GLY321 |
site_id | BC6 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE LYS B 420 |
Chain | Residue |
B | LEU118 |
B | ARG134 |
B | LEU167 |
B | SER169 |
B | TYR290 |
B | ASP293 |
B | ASP330 |
B | SAM417 |
B | PLP419 |
B | HOH597 |
site_id | BC7 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP B 419 |
Chain | Residue |
A | SER320 |
A | GLY321 |
B | THR110 |
B | TYR113 |
B | ARG116 |
B | ARG198 |
B | TYR287 |
B | TYR288 |
B | LYS337 |
B | LYS420 |
B | HOH499 |
B | HOH503 |
B | HOH518 |
B | HOH592 |
B | HOH607 |
site_id | BC8 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE LYS C 420 |
Chain | Residue |
C | LEU118 |
C | ARG134 |
C | LEU167 |
C | SER169 |
C | TYR290 |
C | ASP293 |
C | ASP330 |
C | SAM417 |
C | PLP419 |
C | HOH617 |
site_id | BC9 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE PLP C 419 |
Chain | Residue |
C | THR110 |
C | TYR113 |
C | ARG116 |
C | LEU118 |
C | ARG198 |
C | TYR287 |
C | TYR288 |
C | LYS337 |
C | LYS420 |
C | HOH597 |
C | HOH601 |
C | HOH606 |
C | HOH626 |
C | HOH769 |
D | SER320 |
D | GLY321 |
site_id | CC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE LYS D 420 |
Chain | Residue |
D | LEU118 |
D | ARG134 |
D | LEU167 |
D | SER169 |
D | TYR290 |
D | ASP293 |
D | ASP330 |
D | SAM417 |
D | PLP419 |
D | HOH640 |
site_id | CC2 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE PLP D 419 |
Chain | Residue |
C | SER320 |
C | GLY321 |
D | THR110 |
D | TYR113 |
D | ARG116 |
D | LEU118 |
D | ARG198 |
D | TYR287 |
D | TYR288 |
D | LYS337 |
D | LYS420 |
D | HOH498 |
D | HOH502 |
D | HOH659 |
D | HOH660 |
site_id | CC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 A 418 |
Chain | Residue |
A | CYS125 |
A | CYS129 |
A | CYS132 |
A | GLY171 |
A | ARG202 |
A | HIS230 |
A | SAM417 |
site_id | CC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 B 418 |
Chain | Residue |
B | CYS125 |
B | CYS129 |
B | CYS132 |
B | GLY171 |
B | ARG202 |
B | HIS230 |
B | SAM417 |
site_id | CC5 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 C 418 |
Chain | Residue |
C | CYS125 |
C | CYS129 |
C | CYS132 |
C | GLY171 |
C | ARG202 |
C | HIS230 |
C | SAM417 |
site_id | CC6 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SF4 D 418 |
Chain | Residue |
D | CYS125 |
D | CYS129 |
D | CYS132 |
D | GLY171 |
D | ARG202 |
D | HIS230 |
D | SAM417 |
D | HOH608 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 28 |
Details | BINDING: |
Chain | Residue | Details |
A | CYS125 | |
B | CYS132 | |
B | CYS268 | |
B | CYS375 | |
B | CYS377 | |
B | CYS380 | |
C | CYS125 | |
C | CYS129 | |
C | CYS132 | |
C | CYS268 | |
C | CYS375 | |
A | CYS129 | |
C | CYS377 | |
C | CYS380 | |
D | CYS125 | |
D | CYS129 | |
D | CYS132 | |
D | CYS268 | |
D | CYS375 | |
D | CYS377 | |
D | CYS380 | |
A | CYS132 | |
A | CYS268 | |
A | CYS375 | |
A | CYS377 | |
A | CYS380 | |
B | CYS125 | |
B | CYS129 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | MOD_RES: N6-(pyridoxal phosphate)lysine |
Chain | Residue | Details |
A | LYS337 | |
B | LYS337 | |
C | LYS337 | |
D | LYS337 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 10 |
Details | M-CSA 358 |
Chain | Residue | Details |
A | ARG112 | electrostatic stabiliser, hydrogen bond donor, steric role |
A | LYS337 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
A | TYR113 | electrostatic stabiliser, hydrogen bond donor, steric role |
A | ARG116 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
A | CYS125 | activator, metal ligand |
A | CYS129 | activator, metal ligand |
A | CYS132 | activator, metal ligand |
A | ARG134 | electrostatic stabiliser, hydrogen bond donor, steric role |
A | ASP293 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
A | ASP330 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
site_id | MCSA2 |
Number of Residues | 10 |
Details | M-CSA 358 |
Chain | Residue | Details |
B | ARG112 | electrostatic stabiliser, hydrogen bond donor, steric role |
B | LYS337 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
B | TYR113 | electrostatic stabiliser, hydrogen bond donor, steric role |
B | ARG116 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
B | CYS125 | activator, metal ligand |
B | CYS129 | activator, metal ligand |
B | CYS132 | activator, metal ligand |
B | ARG134 | electrostatic stabiliser, hydrogen bond donor, steric role |
B | ASP293 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
B | ASP330 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
site_id | MCSA3 |
Number of Residues | 10 |
Details | M-CSA 358 |
Chain | Residue | Details |
C | ARG112 | electrostatic stabiliser, hydrogen bond donor, steric role |
C | LYS337 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
C | TYR113 | electrostatic stabiliser, hydrogen bond donor, steric role |
C | ARG116 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
C | CYS125 | activator, metal ligand |
C | CYS129 | activator, metal ligand |
C | CYS132 | activator, metal ligand |
C | ARG134 | electrostatic stabiliser, hydrogen bond donor, steric role |
C | ASP293 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
C | ASP330 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
site_id | MCSA4 |
Number of Residues | 10 |
Details | M-CSA 358 |
Chain | Residue | Details |
D | ARG112 | electrostatic stabiliser, hydrogen bond donor, steric role |
D | LYS337 | covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor |
D | TYR113 | electrostatic stabiliser, hydrogen bond donor, steric role |
D | ARG116 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
D | CYS125 | activator, metal ligand |
D | CYS129 | activator, metal ligand |
D | CYS132 | activator, metal ligand |
D | ARG134 | electrostatic stabiliser, hydrogen bond donor, steric role |
D | ASP293 | electrostatic stabiliser, hydrogen bond acceptor, steric role |
D | ASP330 | electrostatic stabiliser, hydrogen bond acceptor, steric role |