2RK8
The Structure of rat cytosolic PEPCK in complex with phosphonoformate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| A | 0004611 | molecular_function | phosphoenolpyruvate carboxykinase activity |
| A | 0004613 | molecular_function | phosphoenolpyruvate carboxykinase (GTP) activity |
| A | 0005525 | molecular_function | GTP binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005783 | cellular_component | endoplasmic reticulum |
| A | 0005829 | cellular_component | cytosol |
| A | 0006006 | biological_process | glucose metabolic process |
| A | 0006094 | biological_process | gluconeogenesis |
| A | 0006107 | biological_process | oxaloacetate metabolic process |
| A | 0006629 | biological_process | lipid metabolic process |
| A | 0009617 | biological_process | response to bacterium |
| A | 0014823 | biological_process | response to activity |
| A | 0016301 | molecular_function | kinase activity |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0017076 | molecular_function | purine nucleotide binding |
| A | 0018105 | biological_process | peptidyl-serine phosphorylation |
| A | 0019003 | molecular_function | GDP binding |
| A | 0019543 | biological_process | propionate catabolic process |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0031406 | molecular_function | carboxylic acid binding |
| A | 0031667 | biological_process | response to nutrient levels |
| A | 0032496 | biological_process | response to lipopolysaccharide |
| A | 0032868 | biological_process | response to insulin |
| A | 0032869 | biological_process | cellular response to insulin stimulus |
| A | 0033993 | biological_process | response to lipid |
| A | 0042593 | biological_process | glucose homeostasis |
| A | 0042594 | biological_process | response to starvation |
| A | 0043382 | biological_process | positive regulation of memory T cell differentiation |
| A | 0043648 | biological_process | dicarboxylic acid metabolic process |
| A | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| A | 0046166 | biological_process | glyceraldehyde-3-phosphate biosynthetic process |
| A | 0046327 | biological_process | glycerol biosynthetic process from pyruvate |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0046889 | biological_process | positive regulation of lipid biosynthetic process |
| A | 0046890 | biological_process | regulation of lipid biosynthetic process |
| A | 0051365 | biological_process | cellular response to potassium ion starvation |
| A | 0070365 | biological_process | hepatocyte differentiation |
| A | 0070741 | biological_process | response to interleukin-6 |
| A | 0071300 | biological_process | cellular response to retinoic acid |
| A | 0071320 | biological_process | cellular response to cAMP |
| A | 0071332 | biological_process | cellular response to fructose stimulus |
| A | 0071333 | biological_process | cellular response to glucose stimulus |
| A | 0071347 | biological_process | cellular response to interleukin-1 |
| A | 0071356 | biological_process | cellular response to tumor necrosis factor |
| A | 0071377 | biological_process | cellular response to glucagon stimulus |
| A | 0071456 | biological_process | cellular response to hypoxia |
| A | 0071474 | biological_process | cellular hyperosmotic response |
| A | 0071475 | biological_process | cellular hyperosmotic salinity response |
| A | 0071476 | biological_process | cellular hypotonic response |
| A | 0071477 | biological_process | cellular hypotonic salinity response |
| A | 0071549 | biological_process | cellular response to dexamethasone stimulus |
| A | 0072350 | biological_process | tricarboxylic acid metabolic process |
| A | 0097403 | biological_process | cellular response to raffinose |
| A | 0106264 | molecular_function | protein serine kinase activity (using GTP as donor) |
| A | 1904628 | biological_process | cellular response to phorbol 13-acetate 12-myristate |
| A | 1904640 | biological_process | response to methionine |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0004550 | molecular_function | nucleoside diphosphate kinase activity |
| B | 0004611 | molecular_function | phosphoenolpyruvate carboxykinase activity |
| B | 0004613 | molecular_function | phosphoenolpyruvate carboxykinase (GTP) activity |
| B | 0005525 | molecular_function | GTP binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005783 | cellular_component | endoplasmic reticulum |
| B | 0005829 | cellular_component | cytosol |
| B | 0006006 | biological_process | glucose metabolic process |
| B | 0006094 | biological_process | gluconeogenesis |
| B | 0006107 | biological_process | oxaloacetate metabolic process |
| B | 0006629 | biological_process | lipid metabolic process |
| B | 0009617 | biological_process | response to bacterium |
| B | 0014823 | biological_process | response to activity |
| B | 0016301 | molecular_function | kinase activity |
| B | 0016831 | molecular_function | carboxy-lyase activity |
| B | 0017076 | molecular_function | purine nucleotide binding |
| B | 0018105 | biological_process | peptidyl-serine phosphorylation |
| B | 0019003 | molecular_function | GDP binding |
| B | 0019543 | biological_process | propionate catabolic process |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0031406 | molecular_function | carboxylic acid binding |
| B | 0031667 | biological_process | response to nutrient levels |
| B | 0032496 | biological_process | response to lipopolysaccharide |
| B | 0032868 | biological_process | response to insulin |
| B | 0032869 | biological_process | cellular response to insulin stimulus |
| B | 0033993 | biological_process | response to lipid |
| B | 0042593 | biological_process | glucose homeostasis |
| B | 0042594 | biological_process | response to starvation |
| B | 0043382 | biological_process | positive regulation of memory T cell differentiation |
| B | 0043648 | biological_process | dicarboxylic acid metabolic process |
| B | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| B | 0046166 | biological_process | glyceraldehyde-3-phosphate biosynthetic process |
| B | 0046327 | biological_process | glycerol biosynthetic process from pyruvate |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0046889 | biological_process | positive regulation of lipid biosynthetic process |
| B | 0046890 | biological_process | regulation of lipid biosynthetic process |
| B | 0051365 | biological_process | cellular response to potassium ion starvation |
| B | 0070365 | biological_process | hepatocyte differentiation |
| B | 0070741 | biological_process | response to interleukin-6 |
| B | 0071300 | biological_process | cellular response to retinoic acid |
| B | 0071320 | biological_process | cellular response to cAMP |
| B | 0071332 | biological_process | cellular response to fructose stimulus |
| B | 0071333 | biological_process | cellular response to glucose stimulus |
| B | 0071347 | biological_process | cellular response to interleukin-1 |
| B | 0071356 | biological_process | cellular response to tumor necrosis factor |
| B | 0071377 | biological_process | cellular response to glucagon stimulus |
| B | 0071456 | biological_process | cellular response to hypoxia |
| B | 0071474 | biological_process | cellular hyperosmotic response |
| B | 0071475 | biological_process | cellular hyperosmotic salinity response |
| B | 0071476 | biological_process | cellular hypotonic response |
| B | 0071477 | biological_process | cellular hypotonic salinity response |
| B | 0071549 | biological_process | cellular response to dexamethasone stimulus |
| B | 0072350 | biological_process | tricarboxylic acid metabolic process |
| B | 0097403 | biological_process | cellular response to raffinose |
| B | 0106264 | molecular_function | protein serine kinase activity (using GTP as donor) |
| B | 1904628 | biological_process | cellular response to phorbol 13-acetate 12-myristate |
| B | 1904640 | biological_process | response to methionine |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN A 700 |
| Chain | Residue |
| A | LYS244 |
| A | HIS264 |
| A | ASP311 |
| A | PPF3969 |
| A | HOH5803 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 624 |
| Chain | Residue |
| A | HOH5930 |
| A | HOH6047 |
| A | VAL65 |
| A | LEU79 |
| A | ASN208 |
| A | HOH5839 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN B 700 |
| Chain | Residue |
| B | LYS244 |
| B | HIS264 |
| B | ASP311 |
| B | PPF3969 |
| B | HOH4040 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 624 |
| Chain | Residue |
| B | LEU79 |
| B | ASN208 |
| B | HOH3970 |
| B | HOH4138 |
| B | HOH4249 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE PPF A 3969 |
| Chain | Residue |
| A | ARG87 |
| A | LYS244 |
| A | HIS264 |
| A | SER286 |
| A | ASP311 |
| A | PHE333 |
| A | ARG405 |
| A | MN700 |
| A | HOH5786 |
| A | HOH5803 |
| A | HOH5924 |
| A | HOH5943 |
| A | HOH6055 |
| site_id | AC6 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PPF B 3969 |
| Chain | Residue |
| B | ARG87 |
| B | LYS244 |
| B | HIS264 |
| B | SER286 |
| B | ASP311 |
| B | ARG405 |
| B | MN700 |
| B | HOH4040 |
| B | HOH4161 |
| B | HOH4203 |
| B | HOH4257 |
| B | HOH4360 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE FMT A 3406 |
| Chain | Residue |
| A | ALA287 |
| A | GLY289 |
| A | ARG436 |
| A | HOH5914 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PEG A 5759 |
| Chain | Residue |
| A | ASN7 |
| A | ASP10 |
| A | PHE11 |
| A | LYS14 |
| A | GLN39 |
| A | HOH6143 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE FMT B 3406 |
| Chain | Residue |
| B | TYR235 |
| B | GLY236 |
| B | GLY237 |
| B | ASN403 |
| B | ARG405 |
| B | HOH4257 |
Functional Information from PROSITE/UniProt
| site_id | PS00505 |
| Number of Residues | 9 |
| Details | PEPCK_GTP Phosphoenolpyruvate carboxykinase (GTP) signature. FPSACGKTN |
| Chain | Residue | Details |
| A | PHE284-ASN292 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: ACT_SITE => ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:2909519 |
| Chain | Residue | Details |
| A | CYS288 | |
| B | CYS288 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17685635, ECO:0000269|PubMed:18772387, ECO:0000269|PubMed:20476774, ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:24863970 |
| Chain | Residue | Details |
| A | ARG87 | |
| B | ARG87 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:18197707, ECO:0000269|PubMed:18772387, ECO:0000269|PubMed:20476774, ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:24863970 |
| Chain | Residue | Details |
| A | TYR235 | |
| A | ASN403 | |
| B | TYR235 | |
| B | ASN403 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17685635, ECO:0000269|PubMed:18197707, ECO:0000269|PubMed:18772387, ECO:0000269|PubMed:20476774, ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:24863970, ECO:0000269|PubMed:26322521, ECO:0000269|PubMed:26709450, ECO:0000269|PubMed:28345895, ECO:0000269|PubMed:31461616, ECO:0007744|PDB:4YW9, ECO:0007744|PDB:5FH0, ECO:0007744|PDB:5FH1, ECO:0007744|PDB:5FH2, ECO:0007744|PDB:5FH3, ECO:0007744|PDB:5FH4, ECO:0007744|PDB:5FH5, ECO:0007744|PDB:5V97, ECO:0007744|PDB:5V9F, ECO:0007744|PDB:5V9G, ECO:0007744|PDB:6P5O |
| Chain | Residue | Details |
| A | LYS244 | |
| A | HIS264 | |
| A | ASP311 | |
| B | LYS244 | |
| B | HIS264 | |
| B | ASP311 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17685635, ECO:0000269|PubMed:18197707, ECO:0000269|PubMed:18772387, ECO:0000269|PubMed:20476774, ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:24863970 |
| Chain | Residue | Details |
| A | SER286 | |
| B | SER286 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17685635, ECO:0000269|PubMed:18772387, ECO:0000269|PubMed:20476774, ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:24863970, ECO:0000269|PubMed:26322521, ECO:0000269|PubMed:26709450, ECO:0000269|PubMed:28345895, ECO:0007744|PDB:4YW9, ECO:0007744|PDB:5FH0, ECO:0007744|PDB:5FH1, ECO:0007744|PDB:5FH2, ECO:0007744|PDB:5FH3, ECO:0007744|PDB:5FH4, ECO:0007744|PDB:5V97, ECO:0007744|PDB:5V9F, ECO:0007744|PDB:5V9G |
| Chain | Residue | Details |
| A | ALA287 | |
| A | ARG436 | |
| A | PHE530 | |
| B | ALA287 | |
| B | ARG436 | |
| B | PHE530 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:17685635, ECO:0000269|PubMed:20476774, ECO:0000269|PubMed:23127136, ECO:0000269|PubMed:24863970, ECO:0000269|PubMed:26322521, ECO:0000269|PubMed:26709450, ECO:0000269|PubMed:28345895, ECO:0007744|PDB:4YW9, ECO:0007744|PDB:5FH0, ECO:0007744|PDB:5FH1, ECO:0007744|PDB:5FH2, ECO:0007744|PDB:5FH3, ECO:0007744|PDB:5FH4, ECO:0007744|PDB:5V97, ECO:0007744|PDB:5V9F, ECO:0007744|PDB:5V9G |
| Chain | Residue | Details |
| A | ARG405 | |
| B | ARG405 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:22673903 |
| Chain | Residue | Details |
| A | SER19 | |
| A | SER118 | |
| B | SER19 | |
| B | SER118 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-acetyllysine; by p300/EP300 => ECO:0000250|UniProtKB:P35558 |
| Chain | Residue | Details |
| A | LYS70 | |
| A | LYS71 | |
| A | LYS594 | |
| B | LYS70 | |
| B | LYS71 | |
| B | LYS594 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P35558 |
| Chain | Residue | Details |
| A | SER90 | |
| B | SER90 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-acetyllysine; by p300/EP300 => ECO:0000250|UniProtKB:P35558, ECO:0000269|PubMed:30193097 |
| Chain | Residue | Details |
| A | LYS91 | |
| B | LYS91 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q16822 |
| Chain | Residue | Details |
| A | THR178 | |
| B | THR178 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q16822 |
| Chain | Residue | Details |
| A | SER286 | |
| B | SER286 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000269|PubMed:30193097 |
| Chain | Residue | Details |
| A | LYS473 | |
| A | LYS521 | |
| A | LYS524 | |
| B | LYS473 | |
| B | LYS521 | |
| B | LYS524 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1aq2 |
| Chain | Residue | Details |
| A | HIS264 | |
| A | LYS290 | |
| A | ARG405 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1aq2 |
| Chain | Residue | Details |
| B | HIS264 | |
| B | LYS290 | |
| B | ARG405 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1aq2 |
| Chain | Residue | Details |
| A | HIS264 | |
| A | ARG405 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1aq2 |
| Chain | Residue | Details |
| B | HIS264 | |
| B | ARG405 |
