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(-) Description

Title :  STRUCTURE OF STAPHYLOCOCCUS AUREUS D-TAGATOSE-6-PHOSPHATE KINASE IN COMPLEX WITH ADP
 
Authors :  L. Miallau, W. N. Hunter, S. M. Mcsweeney, G. A. Leonard
Date :  16 Feb 07  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  D-Tagatose-6-Phosphate Kinase, Phosphoryl Transfer, Conformational Changes, Kinase, Transferase, Lactose Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Miallau, W. N. Hunter, S. M. Mcsweeney, G. A. Leonard
Structures Of Staphylococcus Aureus D-Tagatose-6- Phosphate Kinase Implicate Domain Motions In Specificity And Mechanism.
J. Biol. Chem. V. 282 19948 2007
PubMed-ID: 17459874  |  Reference-DOI: 10.1074/JBC.M701480200

(-) Compounds

Molecule 1 - TAGATOSE-6-PHOSPHATE KINASE
    ChainsA, B, C, D
    EC Number2.7.1.144
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET15B
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid93061
    StrainNCTC 8325
    SynonymPHOSPHOTAGATOKINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:222 , ALA B:225 , GLY B:227 , ILE B:241 , ILE B:244 , PRO B:249 , GLY B:251 , SER B:252 , GLY B:253 , THR B:256 , ASN B:278 , GLY B:281 , MSE B:282 , HOH B:2105 , HOH B:2114 , HOH B:2146 , HOH B:2147BINDING SITE FOR RESIDUE ADP B1311
2AC2SOFTWARESER D:222 , GLY D:224 , GLY D:227 , ILE D:244 , VAL D:246 , PRO D:249 , SER D:252 , GLY D:253 , THR D:256 , ASN D:278 , GLY D:281 , MSE D:282 , HOH D:2106 , HOH D:2120 , HOH D:2121 , HOH D:2122 , HOH D:2123BINDING SITE FOR RESIDUE ADP D1311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JGV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JGV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JGV)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.LACC_STAA836-60
 
 
 
  4A:36-60
B:36-60
C:36-60
D:36-60
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.LACC_STAA8248-261
 
 
 
  4A:248-261
B:248-261
C:248-261
D:248-261
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.LACC_STAA836-60
 
 
 
  2A:36-60
-
-
D:36-60
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.LACC_STAA8248-261
 
 
 
  2A:248-261
-
-
D:248-261
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.LACC_STAA836-60
 
 
 
  2-
B:36-60
C:36-60
-
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.LACC_STAA8248-261
 
 
 
  2-
B:248-261
C:248-261
-

(-) Exons   (0, 0)

(no "Exon" information available for 2JGV)

(-) 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:315
 aligned with LACC_STAA8 | P0A0B9 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:315
                                 1                                                                                                                                                                                                                                                                                                                     
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305     
           LACC_STAA8     - -----MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2jgva_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh..ee..eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhh...eeee.hhhhhhhhhh......ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jgv A  -4 PRGSHmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275      |285       295       305     
                                 1-MSE                                                                                                                                                                                                                                                                                  282-MSE                        

Chain B from PDB  Type:PROTEIN  Length:314
 aligned with LACC_STAA8 | P0A0B9 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:314
                                1                                                                                                                                                                                                                                                                                                                     
                                |    6        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    
           LACC_STAA8     - ----MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2jgvb_ B: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh..ee..eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhh...eeee.hhhhhhhhhhh.....ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jgv B  -3 RGSHmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
                                |    6        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    
                                1-MSE                                                                                                                                                                                                                                                                                  282-MSE                        

Chain C from PDB  Type:PROTEIN  Length:311
 aligned with LACC_STAA8 | P0A0B9 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:311
                             1                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
           LACC_STAA8     - -MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2jgvc_ C: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhh..ee..eee....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhh...eeee.hhhhhhhhhh......ee..hhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeee..eeeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jgv C   0 HmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  |    289       299       309 
                             1-MSE                                                                                                                                                                                                                                                                                  282-MSE                        

Chain D from PDB  Type:PROTEIN  Length:311
 aligned with LACC_STAA8 | P0A0B9 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:311
                             1                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
           LACC_STAA8     - -MILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGMLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
               SCOP domains d2jgvd_ D: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PfkB-2jgvD01 D:5-297                                                                                                                                                                                                                                                                                 ------------- Pfam domains (1)
           Pfam domains (2) -----PfkB-2jgvD02 D:5-297                                                                                                                                                                                                                                                                                 ------------- Pfam domains (2)
           Pfam domains (3) -----PfkB-2jgvD03 D:5-297                                                                                                                                                                                                                                                                                 ------------- Pfam domains (3)
           Pfam domains (4) -----PfkB-2jgvD04 D:5-297                                                                                                                                                                                                                                                                                 ------------- Pfam domains (4)
         Sec.struct. author ..eeeee...eeeeeeee.......eeee...eeeeehhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh..ee..ee.....eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhh..eeee..hhhhhhhhh......ee..hhhhhhhhh......hhhhhhhhhhhhhhh...eeeee.hhh.eeeee..eeeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhh..eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PFKB_KINASES_1           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jgv D   0 HmILTLTLNPSVDISYPLTALKLDDVNRVQEVSKTAGGKGLNVTRVLAQVGEPVLASGFIGGELGQFIAKKLDHADIKHAFYNIKGETRNCIAILHEGQQTEILEQGPEIDNQEAAGFIKHFEQLLEKVEAVAISGSLPKGLNQDYYAQIIERCQNKGVPVILDCSGATLQTVLENPYKPTVIKPNISELYQLLNQPLDESLESLKQAVSQPLFEGIEWIIVSLGAQGAFAKHNHTFYRVNIPTISVLNPVGSGDSTVAGITSAILNHENDHDLLKKANTLGmLNAQEAQTGYVNLNNYDDLFNQIEVLEV 310
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279  |    289       299       309 
                             1-MSE                                                                                                                                                                                                                                                                                  282-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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JGV)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LACC_STAA8 | P0A0B9)
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:0009024    tagatose-6-phosphate kinase activity    Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
    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:2001059    D-tagatose 6-phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a D-tagatose 6-phosphate.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019512    lactose catabolic process via tagatose-6-phosphate    The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate.
    GO:0005988    lactose metabolic process    The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        LACC_STAA8 | P0A0B92jg1

(-) Related Entries Specified in the PDB File

2jg1 STRUCTURE OF STAPHYLOCOCCUS AUREUS D-TAGATOSE -6-PHOSPHATE KINASE WITH COFACTOR AND SUBSTRATE