3EZW
Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices
Replaces: 2P3RFunctional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004370 | molecular_function | glycerol kinase activity |
A | 0005515 | molecular_function | protein binding |
A | 0005524 | molecular_function | ATP binding |
A | 0005829 | cellular_component | cytosol |
A | 0005975 | biological_process | carbohydrate metabolic process |
A | 0006071 | biological_process | glycerol metabolic process |
A | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
A | 0006974 | biological_process | DNA damage response |
A | 0008270 | molecular_function | zinc ion binding |
A | 0016301 | molecular_function | kinase activity |
A | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
A | 0019563 | biological_process | glycerol catabolic process |
A | 0042802 | molecular_function | identical protein binding |
A | 0046872 | molecular_function | metal ion binding |
B | 0004370 | molecular_function | glycerol kinase activity |
B | 0005515 | molecular_function | protein binding |
B | 0005524 | molecular_function | ATP binding |
B | 0005829 | cellular_component | cytosol |
B | 0005975 | biological_process | carbohydrate metabolic process |
B | 0006071 | biological_process | glycerol metabolic process |
B | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
B | 0006974 | biological_process | DNA damage response |
B | 0008270 | molecular_function | zinc ion binding |
B | 0016301 | molecular_function | kinase activity |
B | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
B | 0019563 | biological_process | glycerol catabolic process |
B | 0042802 | molecular_function | identical protein binding |
B | 0046872 | molecular_function | metal ion binding |
C | 0004370 | molecular_function | glycerol kinase activity |
C | 0005515 | molecular_function | protein binding |
C | 0005524 | molecular_function | ATP binding |
C | 0005829 | cellular_component | cytosol |
C | 0005975 | biological_process | carbohydrate metabolic process |
C | 0006071 | biological_process | glycerol metabolic process |
C | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
C | 0006974 | biological_process | DNA damage response |
C | 0008270 | molecular_function | zinc ion binding |
C | 0016301 | molecular_function | kinase activity |
C | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
C | 0019563 | biological_process | glycerol catabolic process |
C | 0042802 | molecular_function | identical protein binding |
C | 0046872 | molecular_function | metal ion binding |
D | 0004370 | molecular_function | glycerol kinase activity |
D | 0005515 | molecular_function | protein binding |
D | 0005524 | molecular_function | ATP binding |
D | 0005829 | cellular_component | cytosol |
D | 0005975 | biological_process | carbohydrate metabolic process |
D | 0006071 | biological_process | glycerol metabolic process |
D | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
D | 0006974 | biological_process | DNA damage response |
D | 0008270 | molecular_function | zinc ion binding |
D | 0016301 | molecular_function | kinase activity |
D | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
D | 0019563 | biological_process | glycerol catabolic process |
D | 0042802 | molecular_function | identical protein binding |
D | 0046872 | molecular_function | metal ion binding |
E | 0004370 | molecular_function | glycerol kinase activity |
E | 0005515 | molecular_function | protein binding |
E | 0005524 | molecular_function | ATP binding |
E | 0005829 | cellular_component | cytosol |
E | 0005975 | biological_process | carbohydrate metabolic process |
E | 0006071 | biological_process | glycerol metabolic process |
E | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
E | 0006974 | biological_process | DNA damage response |
E | 0008270 | molecular_function | zinc ion binding |
E | 0016301 | molecular_function | kinase activity |
E | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
E | 0019563 | biological_process | glycerol catabolic process |
E | 0042802 | molecular_function | identical protein binding |
E | 0046872 | molecular_function | metal ion binding |
F | 0004370 | molecular_function | glycerol kinase activity |
F | 0005515 | molecular_function | protein binding |
F | 0005524 | molecular_function | ATP binding |
F | 0005829 | cellular_component | cytosol |
F | 0005975 | biological_process | carbohydrate metabolic process |
F | 0006071 | biological_process | glycerol metabolic process |
F | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
F | 0006974 | biological_process | DNA damage response |
F | 0008270 | molecular_function | zinc ion binding |
F | 0016301 | molecular_function | kinase activity |
F | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
F | 0019563 | biological_process | glycerol catabolic process |
F | 0042802 | molecular_function | identical protein binding |
F | 0046872 | molecular_function | metal ion binding |
G | 0004370 | molecular_function | glycerol kinase activity |
G | 0005515 | molecular_function | protein binding |
G | 0005524 | molecular_function | ATP binding |
G | 0005829 | cellular_component | cytosol |
G | 0005975 | biological_process | carbohydrate metabolic process |
G | 0006071 | biological_process | glycerol metabolic process |
G | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
G | 0006974 | biological_process | DNA damage response |
G | 0008270 | molecular_function | zinc ion binding |
G | 0016301 | molecular_function | kinase activity |
G | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
G | 0019563 | biological_process | glycerol catabolic process |
G | 0042802 | molecular_function | identical protein binding |
G | 0046872 | molecular_function | metal ion binding |
H | 0004370 | molecular_function | glycerol kinase activity |
H | 0005515 | molecular_function | protein binding |
H | 0005524 | molecular_function | ATP binding |
H | 0005829 | cellular_component | cytosol |
H | 0005975 | biological_process | carbohydrate metabolic process |
H | 0006071 | biological_process | glycerol metabolic process |
H | 0006072 | biological_process | glycerol-3-phosphate metabolic process |
H | 0006974 | biological_process | DNA damage response |
H | 0008270 | molecular_function | zinc ion binding |
H | 0016301 | molecular_function | kinase activity |
H | 0016773 | molecular_function | phosphotransferase activity, alcohol group as acceptor |
H | 0019563 | biological_process | glycerol catabolic process |
H | 0042802 | molecular_function | identical protein binding |
H | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL A2647 |
Chain | Residue |
A | ARG83 |
A | GLU84 |
A | TRP103 |
A | TYR135 |
A | ASP245 |
A | GLN246 |
A | PHE270 |
A | HOH9042 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL A2648 |
Chain | Residue |
A | VAL178 |
A | GLN226 |
A | HOH9099 |
C | HOH2663 |
A | ARG177 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE MG A2649 |
Chain | Residue |
A | ASP72 |
A | HOH9000 |
A | HOH9001 |
A | HOH9002 |
A | HOH9003 |
G | HOH9000 |
site_id | AC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO A2650 |
Chain | Residue |
A | HIS195 |
A | GLU277 |
A | LYS278 |
A | ALA279 |
A | TYR300 |
site_id | AC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO A2651 |
Chain | Residue |
A | ALA353 |
A | TYR355 |
A | GLN387 |
A | ASP390 |
A | TRP486 |
A | HOH9100 |
site_id | AC6 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL B2648 |
Chain | Residue |
B | GLN82 |
B | ARG83 |
B | GLU84 |
B | TRP103 |
B | TYR135 |
B | ASP245 |
B | GLN246 |
B | PHE270 |
B | HOH2670 |
B | HOH2674 |
site_id | AC7 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL B2649 |
Chain | Residue |
B | ARG177 |
B | GLY225 |
B | GLN226 |
site_id | AC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO B2650 |
Chain | Residue |
B | HIS195 |
B | GLU277 |
B | ALA279 |
B | TYR300 |
E | ARG117 |
site_id | AC9 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE EDO B2651 |
Chain | Residue |
B | CYS112 |
B | LYS116 |
B | ILE132 |
B | ASP133 |
B | PRO134 |
B | PRO358 |
B | HOH2687 |
B | HOH2792 |
B | HOH2838 |
site_id | BC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL E2641 |
Chain | Residue |
E | ARG83 |
E | GLU84 |
E | TRP103 |
E | TYR135 |
E | ASP245 |
E | GLN246 |
E | PHE270 |
E | HOH2746 |
site_id | BC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL E2642 |
Chain | Residue |
E | ARG177 |
E | GLY225 |
E | GLN226 |
site_id | BC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO E2643 |
Chain | Residue |
E | GLU121 |
E | ARG125 |
E | HOH2646 |
E | HOH2655 |
E | HOH2714 |
site_id | BC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL G2643 |
Chain | Residue |
G | ARG83 |
G | GLU84 |
G | TRP103 |
G | TYR135 |
G | ASP245 |
G | GLN246 |
G | HOH9105 |
site_id | BC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL G2644 |
Chain | Residue |
G | ARG177 |
G | VAL178 |
G | GLY225 |
G | GLN226 |
site_id | BC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO G2645 |
Chain | Residue |
G | GLU121 |
G | ARG125 |
G | HOH9016 |
G | HOH9019 |
G | HOH9023 |
G | HOH9160 |
site_id | BC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO G2646 |
Chain | Residue |
G | HIS195 |
G | GLU277 |
G | LYS278 |
G | ALA279 |
G | TYR300 |
site_id | BC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO G2647 |
Chain | Residue |
G | HOH9078 |
G | ALA353 |
G | TYR355 |
G | GLN387 |
G | ASP390 |
site_id | BC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EDO G2648 |
Chain | Residue |
G | THR339 |
G | GLU382 |
G | TYR386 |
G | ARG482 |
site_id | CC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL C2649 |
Chain | Residue |
C | ARG83 |
C | GLU84 |
C | TRP103 |
C | TYR135 |
C | ASP245 |
C | GLN246 |
C | HOH2775 |
site_id | CC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL C2650 |
Chain | Residue |
C | ARG177 |
C | GLY225 |
C | GLN226 |
site_id | CC3 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EDO C2651 |
Chain | Residue |
C | GLU121 |
C | ARG125 |
C | HOH2690 |
C | HOH2705 |
site_id | CC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO C2652 |
Chain | Residue |
C | TRP103 |
C | GLN104 |
C | ARG106 |
C | PHE307 |
C | THR349 |
C | HOH2776 |
site_id | CC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EDO C2653 |
Chain | Residue |
C | HIS195 |
C | LYS278 |
C | ALA279 |
C | TYR300 |
site_id | CC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO C2654 |
Chain | Residue |
C | ASP182 |
C | TYR183 |
C | THR184 |
C | SER220 |
C | GLY296 |
C | GLU297 |
site_id | CC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL D2640 |
Chain | Residue |
D | ARG83 |
D | GLU84 |
D | TRP103 |
D | TYR135 |
D | ASP245 |
D | GLN246 |
D | PHE270 |
D | HOH2709 |
site_id | CC8 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL D2641 |
Chain | Residue |
D | ARG177 |
D | VAL178 |
D | GLN226 |
site_id | CC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO D2642 |
Chain | Residue |
D | TRP103 |
D | GLN104 |
D | ARG106 |
D | PHE307 |
D | THR349 |
D | HOH2743 |
site_id | DC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO D2643 |
Chain | Residue |
D | GLU121 |
D | ARG125 |
D | TRP356 |
D | HOH2671 |
D | HOH2734 |
D | HOH2737 |
site_id | DC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL F2642 |
Chain | Residue |
F | ARG83 |
F | GLU84 |
F | TRP103 |
F | TYR135 |
F | ASP245 |
F | GLN246 |
F | HOH2670 |
site_id | DC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL F2643 |
Chain | Residue |
F | ARG177 |
F | GLN226 |
site_id | DC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE EDO F2644 |
Chain | Residue |
F | HIS195 |
F | LYS278 |
F | ALA279 |
F | TYR300 |
F | HOH2807 |
site_id | DC5 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE EDO F2645 |
Chain | Residue |
F | MET260 |
F | ALA261 |
F | ALA405 |
site_id | DC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL H2644 |
Chain | Residue |
H | ARG83 |
H | GLU84 |
H | TRP103 |
H | TYR135 |
H | ASP245 |
H | GLN246 |
H | HOH2681 |
site_id | DC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL H2645 |
Chain | Residue |
H | ARG177 |
H | GLN226 |
site_id | DC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE EDO H2646 |
Chain | Residue |
H | HIS195 |
H | GLU277 |
H | LYS278 |
H | ALA279 |
H | TYR300 |
H | HOH2799 |
site_id | DC9 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE EDO H2647 |
Chain | Residue |
H | ASP182 |
H | TYR183 |
H | THR184 |
H | ARG219 |
H | SER220 |
H | ALA291 |
H | GLY296 |
H | GLU297 |
Functional Information from PROSITE/UniProt
site_id | PS00445 |
Number of Residues | 21 |
Details | FGGY_KINASES_2 FGGY family of carbohydrate kinases signature 2. GaIFGLtrgvnan.HIIRATLE |
Chain | Residue | Details |
A | GLY362-GLU382 |
site_id | PS00933 |
Number of Residues | 13 |
Details | FGGY_KINASES_1 FGGY family of carbohydrate kinases signature 1. YfSgtKVKWILDH |
Chain | Residue | Details |
A | TYR135-HIS147 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 48 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8170944, ECO:0007744|PDB:1GLC, ECO:0007744|PDB:1GLD, ECO:0007744|PDB:1GLE |
Chain | Residue | Details |
A | THR13 | |
B | TYR135 | |
B | ASP245 | |
B | GLU478 | |
E | THR13 | |
E | ARG83 | |
E | GLU84 | |
E | TYR135 | |
E | ASP245 | |
E | GLU478 | |
G | THR13 | |
A | ARG83 | |
G | ARG83 | |
G | GLU84 | |
G | TYR135 | |
G | ASP245 | |
G | GLU478 | |
C | THR13 | |
C | ARG83 | |
C | GLU84 | |
C | TYR135 | |
C | ASP245 | |
A | GLU84 | |
C | GLU478 | |
D | THR13 | |
D | ARG83 | |
D | GLU84 | |
D | TYR135 | |
D | ASP245 | |
D | GLU478 | |
F | THR13 | |
F | ARG83 | |
F | GLU84 | |
A | TYR135 | |
F | TYR135 | |
F | ASP245 | |
F | GLU478 | |
H | THR13 | |
H | ARG83 | |
H | GLU84 | |
H | TYR135 | |
H | ASP245 | |
H | GLU478 | |
A | ASP245 | |
A | GLU478 | |
B | THR13 | |
B | ARG83 | |
B | GLU84 |
site_id | SWS_FT_FI2 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000305|PubMed:10090737, ECO:0007744|PDB:1BWF, ECO:0007744|PDB:1GLJ, ECO:0007744|PDB:1GLL |
Chain | Residue | Details |
A | THR14 | |
C | GLY411 | |
D | THR14 | |
D | GLY411 | |
F | THR14 | |
F | GLY411 | |
H | THR14 | |
H | GLY411 | |
A | GLY411 | |
B | THR14 | |
B | GLY411 | |
E | THR14 | |
E | GLY411 | |
G | THR14 | |
G | GLY411 | |
C | THR14 |
site_id | SWS_FT_FI3 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000305|PubMed:10090737, ECO:0007744|PDB:1GLJ |
Chain | Residue | Details |
A | SER15 | |
B | SER15 | |
E | SER15 | |
G | SER15 | |
C | SER15 | |
D | SER15 | |
F | SER15 | |
H | SER15 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8170944, ECO:0000269|PubMed:8430315, ECO:0000269|PubMed:9817843, ECO:0007744|PDB:1GLB, ECO:0007744|PDB:1GLD, ECO:0007744|PDB:1GLE, ECO:0007744|PDB:1GLF |
Chain | Residue | Details |
A | ARG17 | |
B | ARG17 | |
E | ARG17 | |
G | ARG17 | |
C | ARG17 | |
D | ARG17 | |
F | ARG17 | |
H | ARG17 |
site_id | SWS_FT_FI5 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9843423, ECO:0007744|PDB:1BO5 |
Chain | Residue | Details |
A | GLY234 | |
C | ARG236 | |
D | GLY234 | |
D | ARG236 | |
F | GLY234 | |
F | ARG236 | |
H | GLY234 | |
H | ARG236 | |
A | ARG236 | |
B | GLY234 | |
B | ARG236 | |
E | GLY234 | |
E | ARG236 | |
G | GLY234 | |
G | ARG236 | |
C | GLY234 |
site_id | SWS_FT_FI6 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8430315, ECO:0000269|PubMed:9843423, ECO:0007744|PDB:1BO5, ECO:0007744|PDB:1BOT |
Chain | Residue | Details |
A | GLN246 | |
B | GLN246 | |
E | GLN246 | |
G | GLN246 | |
C | GLN246 | |
D | GLN246 | |
F | GLN246 | |
H | GLN246 |
site_id | SWS_FT_FI7 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000305|PubMed:10090737, ECO:0007744|PDB:1BWF, ECO:0007744|PDB:1GLL |
Chain | Residue | Details |
A | THR267 | |
G | THR267 | |
G | GLY310 | |
G | GLN314 | |
C | THR267 | |
C | GLY310 | |
C | GLN314 | |
D | THR267 | |
D | GLY310 | |
D | GLN314 | |
F | THR267 | |
A | GLY310 | |
F | GLY310 | |
F | GLN314 | |
H | THR267 | |
H | GLY310 | |
H | GLN314 | |
A | GLN314 | |
B | THR267 | |
B | GLY310 | |
B | GLN314 | |
E | THR267 | |
E | GLY310 | |
E | GLN314 |
site_id | SWS_FT_FI8 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:8170944, ECO:0000269|PubMed:8430315, ECO:0007744|PDB:1GLB, ECO:0007744|PDB:1GLC, ECO:0007744|PDB:1GLD, ECO:0007744|PDB:1GLE |
Chain | Residue | Details |
A | ASN415 | |
B | ASN415 | |
E | ASN415 | |
G | ASN415 | |
C | ASN415 | |
D | ASN415 | |
F | ASN415 | |
H | ASN415 |
site_id | SWS_FT_FI9 |
Number of Residues | 8 |
Details | MOD_RES: N6-malonyllysine => ECO:0000269|PubMed:21908771 |
Chain | Residue | Details |
A | LYS232 | |
B | LYS232 | |
E | LYS232 | |
G | LYS232 | |
C | LYS232 | |
D | LYS232 | |
F | LYS232 | |
H | LYS232 |