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Table 1 Catalytic residues associated with phosphoryl transfer

From: The role of the C8 proton of ATP in the catalysis of shikimate kinase and adenylate kinase

Enzyme

SK

AK1A

AK1B

Residue

Interatomic distance (Å)

Residue

Interatomic distance (Å)

Residue

Interatomic distance (Å)

1. C8-H to α-PO4

 

3.666

 

4.153

 

3.729

2. αC = O to C6-NH2

R153

1.893

G177

1.880

NR1

 

3. Thr-OH to C8H

T17

3.273

T23

2.090

T392

1.786

4. Thr-OH to α-PO4

T17

1.758

T23

2.591

T39

5.648

5. Arg-NH1 to C8

R110

4.228

R128

4.781

R972

2.712

6. Arg-α-PO4

R117

2.757

R132

2.136

R44

1.904

7. Lys- γ-PO4

K15

1.882

K21

1.902

K21

1.865

  1. NR = No coordinated residue.
  2. Coordinated to N7.
  3. The amino acid residues making up the “push” mechanism within the active sites of SK and AK1 identified by the inter-atomic distances between the co-crystallized nucleotide analogue and the amino acid residues within the active site. These residues included: the Thr associated with the proton transfer from C8-H to the α-PO4 (SK, Thr17; AK1, Thr 23), the Arg associated with C8 protonation (SK, Arg110; AK1, Arg128), the Arg co-ordinated to the α-PO4 and β-PO4 (SK, Arg117; AK1, Arg132), and the Lys associated with the γ-PO4 protonation (SK, Lys15; AK1, Lys21). The residues identified in the AK1 second nucleotide binding site (AK1B) are: Thr39 (associated with the proton transfer from C8-H to the α-PO4), Arg97 (associated with C8 protonation), Arg44/138 (co-ordinated to the α-PO4 and β-PO4), and Lys21 (associated with the γ-PO4 protonation).