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 | |
| E | ASP245 | |
| E | GLU478 | |
| G | THR13 | |
| G | ARG83 | |
| G | GLU84 | |
| G | TYR135 | |
| G | ASP245 | |
| G | GLU478 | |
| C | THR13 | |
| C | ARG83 | |
| C | GLU84 | |
| C | TYR135 | |
| C | ASP245 | |
| C | GLU478 | |
| D | THR13 | |
| D | ARG83 | |
| D | GLU84 | |
| D | TYR135 | |
| D | ASP245 | |
| D | GLU478 | |
| F | THR13 | |
| F | ARG83 | |
| F | GLU84 | |
| F | TYR135 | |
| F | ASP245 | |
| F | GLU478 | |
| H | THR13 | |
| H | ARG83 | |
| H | GLU84 | |
| H | TYR135 | |
| H | ASP245 | |
| H | GLU478 | |
| B | TYR135 | |
| B | ASP245 | |
| B | GLU478 | |
| E | THR13 | |
| E | ARG83 | |
| E | GLU84 | |
| E | TYR135 | |
| A | ARG83 | |
| A | GLU84 | |
| A | TYR135 | |
| 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 |
