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(-) Description

Title :  CRYSTAL STRUCTURE OF A LIN0012 PROTEIN FROM LISTERIA INNOCUA
 
Authors :  K. Palani, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  25 Sep 09  (Deposition) - 06 Oct 09  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Keywords :  Lin0012, Listeria Innocua, Protein Structure Initiative Ii(Psi Ii), Nysgxrc, 11277E, Structural Genomics, New York Sgx Research Center For Structural Genomics, Atp-Binding, Kinase, Nucleotide-Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Palani, S. K. Burley, S. Swaminathan
Crystal Structure Of A Lin0012 Protein From Listeria Innocua
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIN0012 PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3 (BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LIN0012
    Organism Scientific: LISTERIA INNOCUA
    Organism Taxid: 1642

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 33)

Asymmetric Unit (2, 33)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
2PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 33)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE
2PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 4 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 5 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:89 , LEU A:189 , ALA A:190 , TYR A:191 , LYS A:192 , SER A:193 , LEU A:194 , HOH A:470 , LEU B:189 , LYS B:192 , LEU B:194BINDING SITE FOR RESIDUE PGE A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K17)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K17)

(-) Exons   (0, 0)

(no "Exon" information available for 3K17)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:355
 aligned with Q92FU1_LISIN | Q92FU1 from UniProtKB/TrEMBL  Length:360

    Alignment length:355
                                                                                                                                                                                                                                                                                                                                                                                           360 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   | 
         Q92FU1_LISIN     7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKMVIETELIDQSGAKYGLGSSAAATVAVINALMTKFYPEISMLKKFKLAALSHLVVQGNGSCGDIASCMYGGWIAYTTFDQEWVKHRLAYKSLEWFMKEPWPMLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEIMKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENMGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITE-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhh...eeeeeeeeeeeeeeeee....eee...................hhhhhhhhhhhhhhhhhhhhh......eeeeeee............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeee..hhhhhhhhhh..hhhhhhhh.....eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.......eeeeee.hhhhhhhhhhhhhhh..ee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k17 A   7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKmVIETELIDQSGAKYGLGSSAAATVAVINALmTKFYPEISmLKKFKLAALSHLVVQGNGSCGDIASCmYGGWIAYTTFDQEWVKHRLAYKSLEWFmKEPWPmLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEImKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENmGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITEG 361
                                    16        26        36        46        56        66        76        86        96      |106       116       126       136      |146       156       166   |   176       186       196 |     206       216       226       236       246       256|      266       276       286       296       306  |    316       326       336       346       356     
                                                                                                                          103-MSE                        134-MSE  143-MSE                    170-MSE                     198-MSE |                                                  257-MSE                                             309-MSE                                                
                                                                                                                                                                                                                               204-MSE                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:355
 aligned with Q92FU1_LISIN | Q92FU1 from UniProtKB/TrEMBL  Length:360

    Alignment length:355
                                                                                                                                                                                                                                                                                                                                                                                           360 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   | 
         Q92FU1_LISIN     7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKMVIETELIDQSGAKYGLGSSAAATVAVINALMTKFYPEISMLKKFKLAALSHLVVQGNGSCGDIASCMYGGWIAYTTFDQEWVKHRLAYKSLEWFMKEPWPMLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEIMKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENMGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITE-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhh...eeeeeeeeeeeeeeeee....eee...................hhhhhhhhhhhhhhhhhhhhh......eeeeeee............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeee..hhhhhhhhhh..hhhhhhhh.....eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee........eeeee.hhhhhhhhhhhhhhhh...........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k17 B   7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKmVIETELIDQSGAKYGLGSSAAATVAVINALmTKFYPEISmLKKFKLAALSHLVVQGNGSCGDIASCmYGGWIAYTTFDQEWVKHRLAYKSLEWFmKEPWPmLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEImKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENmGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITEG 361
                                    16        26        36        46        56        66        76        86        96      |106       116       126       136      |146       156       166   |   176       186       196 |     206       216       226       236       246       256|      266       276       286       296       306  |    316       326       336       346       356     
                                                                                                                          103-MSE                        134-MSE  143-MSE                    170-MSE                     198-MSE |                                                  257-MSE                                             309-MSE                                                
                                                                                                                                                                                                                               204-MSE                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:355
 aligned with Q92FU1_LISIN | Q92FU1 from UniProtKB/TrEMBL  Length:360

    Alignment length:355
                                                                                                                                                                                                                                                                                                                                                                                           360 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   | 
         Q92FU1_LISIN     7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKMVIETELIDQSGAKYGLGSSAAATVAVINALMTKFYPEISMLKKFKLAALSHLVVQGNGSCGDIASCMYGGWIAYTTFDQEWVKHRLAYKSLEWFMKEPWPMLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEIMKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENMGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITE-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee..hhhhh...eeeeeeeeeeeeeeeee....eee...................hhhhhhhhhhhhhhhhhhhhh......eeeeeee............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeee..hhhhhhhhh...hhhhhhhh.....eeeee.....eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee.......eeeeee.hhhhhhhhhhhhhhhh.ee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k17 C   7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKmVIETELIDQSGAKYGLGSSAAATVAVINALmTKFYPEISmLKKFKLAALSHLVVQGNGSCGDIASCmYGGWIAYTTFDQEWVKHRLAYKSLEWFmKEPWPmLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEImKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENmGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITEG 361
                                    16        26        36        46        56        66        76        86        96      |106       116       126       136      |146       156       166   |   176       186       196 |     206       216       226       236       246       256|      266       276       286       296       306  |    316       326       336       346       356     
                                                                                                                          103-MSE                        134-MSE  143-MSE                    170-MSE                     198-MSE |                                                  257-MSE                                             309-MSE                                                
                                                                                                                                                                                                                               204-MSE                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:355
 aligned with Q92FU1_LISIN | Q92FU1 from UniProtKB/TrEMBL  Length:360

    Alignment length:355
                                                                                                                                                                                                                                                                                                                                                                                           360 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   | 
         Q92FU1_LISIN     7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKMVIETELIDQSGAKYGLGSSAAATVAVINALMTKFYPEISMLKKFKLAALSHLVVQGNGSCGDIASCMYGGWIAYTTFDQEWVKHRLAYKSLEWFMKEPWPMLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEIMKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENMGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITE-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------GHMP_kinases_N-3k17D01 D:102-173                                        --------------------------------------------------------------------------------------GHMP_kinases_C-3k17D05 D:260-347                                                        -------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------GHMP_kinases_N-3k17D02 D:102-173                                        --------------------------------------------------------------------------------------GHMP_kinases_C-3k17D06 D:260-347                                                        -------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------GHMP_kinases_N-3k17D03 D:102-173                                        --------------------------------------------------------------------------------------GHMP_kinases_C-3k17D07 D:260-347                                                        -------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------GHMP_kinases_N-3k17D04 D:102-173                                        --------------------------------------------------------------------------------------GHMP_kinases_C-3k17D08 D:260-347                                                        -------------- Pfam domains (4)
         Sec.struct. author ..eeeeeeeeeeee..hhhhh...eeeeeeeeeeeeeeeee....eee......................hhhhhhhhhhhhhhhhhh......eeeeeee............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.eeeee..hhhhhhhhh...hhhhhhhh.....eeeee.....eeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..eeee........eeeee.hhhhhhhhhhhhhhh..ee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k17 D   7 NKLQVKIPGKLYVAGEYAVVESGHTAILTAVNRYITLTLEDSERNELWIPHYENPVSWPIGGELKPDGEHWTFTAEAINIATTFLKSEGIELTPVKmVIETELIDQSGAKYGLGSSAAATVAVINALmTKFYPEISmLKKFKLAALSHLVVQGNGSCGDIASCmYGGWIAYTTFDQEWVKHRLAYKSLEWFmKEPWPmLQIETLEEPVPTFSVGWTGTPVSTGKLVSQIHAFKQEDSKNYQHFLTRNNEImKQIIQAFHTKDEELLYSSIKENRRILQELGTKAGVNIETSLLKELADSAENmGGAGKSSGSGGGDCGIAFSKTKELAEKLVNEWEKLGIKHLPFHTGRVQITEG 361
                                    16        26        36        46        56        66        76        86        96      |106       116       126       136      |146       156       166   |   176       186       196 |     206       216       226       236       246       256|      266       276       286       296       306  |    316       326       336       346       356     
                                                                                                                          103-MSE                        134-MSE  143-MSE                    170-MSE                     198-MSE |                                                  257-MSE                                             309-MSE                                                
                                                                                                                                                                                                                               204-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3K17)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K17)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: GHMP_kinases_C] (13)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q92FU1_LISIN | Q92FU1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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