DB code: S00304

RLCP classification 3.103.70035.360 : Transfer
CATH domain 3.40.50.300 : Rossmann fold Catalytic domain
E.C. 2.7.1.71
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.300 : Rossmann fold S00527 S00547 S00548 S00550 S00554 S00555 S00671 S00672 S00676 S00680 S00682 S00913 S00914 S00301 S00302 S00303 S00307 S00308 S00305 S00306 S00309 S00310 S00311 M00114 M00199 D00129 D00130 D00540 M00186

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P10880 Shikimate kinase 2
SK 2
EC 2.7.1.71
Shikimate kinase II
SKII
PF01202 (SKI)
[Graphical View]
Q83AJ3 Shikimate kinase
SK
EC 2.7.1.71
PF01202 (SKI)
[Graphical View] 		NP_820869.1 (Protein)
NC_002971.3 (DNA/RNA sequence)
Q8A2B2 Shikimate kinase
SK
EC 2.7.1.71
PF01202 (SKI)
[Graphical View] 		NP_812305.1 (Protein)
NC_004663.1 (DNA/RNA sequence)

KEGG enzyme name
shikimate kinase
shikimate kinase (phosphorylating)
shikimate kinase II

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P10880 AROL_ERWCH ATP + shikimate = ADP + shikimate 3-phosphate. Monomer. Cytoplasm (Probable). Binds 1 magnesium ion per subunit.
Q83AJ3 AROK_COXBU ATP + shikimate = ADP + shikimate 3-phosphate. Monomer (By similarity). Cytoplasm (Probable). Binds 1 magnesium ion per subunit (By similarity).
Q8A2B2 AROK_BACTN ATP + shikimate = ADP + shikimate 3-phosphate. Monomer (By similarity). Cytoplasm (Probable). Binds 1 magnesium ion per subunit (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00400 Phenylalanine, tyrosine and tryptophan biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00493 C00008 C03175
E.C.
Compound magnesium ATP Shikimate ADP Shikimate 3-phosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,carboxyl group amine group,nucleotide carbohydrate,carboxyl group,phosphate group/phosphate ion
ChEBI 18420
 18420
 		15422
 15422
 		16119
 16119
 		16761
 16761
 		17052
 17052
PubChem 888
 888
 		5957
 5957
 		8742
 8742
 		6022
 6022
 		121947
 121947
1e6cA Unbound Unbound Unbound Unbound Unbound
1e6cB Unbound Unbound Unbound Unbound Unbound
1shkA Unbound Unbound Unbound Unbound Unbound
1shkB Unbound Unbound Unbound Unbound Unbound
2shkA Unbound Unbound Unbound Unbound Unbound
2shkB Bound:_MG_903 Unbound Unbound Bound:ADP Unbound
3trfA Unbound Unbound Unbound Unbound Unbound
3trfB Unbound Unbound Unbound Unbound Unbound
3vaaA Unbound Unbound Unbound Unbound Unbound
3vaaB Unbound Unbound Unbound Unbound Unbound
3vaaC Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [12]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1e6cA ;ASP 34;ARG 120 THR 16;ASP 32(Mg2+ binding) GLY 12;GLY 14; ;THR 16 mutant K15M
1e6cB ;ASP 34;ARG 120 THR 16;ASP 32(Mg2+ binding) GLY 12;GLY 14; ;THR 16 mutant K15M
1shkA LYS 15;ASP 34; THR 16;ASP 32(Mg2+ binding) GLY 12;GLY 14;LYS 15;THR 16 invisible 113-127
1shkB LYS 15;ASP 34; THR 16;ASP 32(Mg2+ binding) GLY 12;GLY 14;LYS 15;THR 16 invisible 113-125
2shkA LYS 15;ASP 34; THR 16;ASP 32(Mg2+ binding) GLY 12;GLY 14;LYS 15;THR 16 invisible 113-127
2shkB LYS 15;ASP 34; THR 16;ASP 32(Mg2+ binding) GLY 12;GLY 14;LYS 15;THR 16 invisible 113-122
3trfA LYS 18;ASP 37;ARG 123 THR 19;ASP 35(Mg2+ binding) GLY 15;GLY 17;LYS 18;THR 19
3trfB LYS 18;ASP 37;ARG 123 THR 19;ASP 35(Mg2+ binding) GLY 15;GLY 17;LYS 18;THR 19
3vaaA LYS 14;ASP 33;ARG 118 THR 15;ASP 31(Mg2+ binding) GLY 11;GLY 13;LYS 14;THR 15
3vaaB LYS 14;ASP 33;ARG 118 THR 15;ASP 31(Mg2+ binding) GLY 11;GLY 13;LYS 14;THR 15
3vaaC LYS 14;ASP 33; THR 15;ASP 31(Mg2+ binding) GLY 11;GLY 13;LYS 14;THR 15 invisible 114-120

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
p.991
[12]
p.784
[17]
p.8541-8542
[18]
p.417-419

References
[1]
Resource
Comments
Medline ID
PubMed ID 1849480
Journal Eur J Biochem
Year 1991
Volume 196
Pages 717-24
Authors Hawkins AR, Smith M
Title Domain structure and interaction within the pentafunctional arom polypeptide.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8682786
Journal J Bacteriol
Year 1996
Volume 178
Pages 3818-28
Authors Vinella D, Gagny B, Joseleau-Petit D, D'Ari R, Cashel M
Title Mecillinam resistance in Escherichia coli is conferred by loss of a second activity of the AroK protein.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID
Journal Acta Crystallogr D Biol Crystallogr
Year 1997
Volume 53
Pages 612-614
Authors Krell T, Coyle JE, Horsburgh MJ, Coggins JR, Lapthorn AJ
Title Crystallization and preliminary x-ray crystallographic analysis of shikimate kinase.
Related PDB 1shk 2shk
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9450055
Journal Biochem Soc Trans
Year 1997
Volume 25
Pages S627
Authors Idziak C, Price NC, Kelly SM, Krell T, Boam DJ, Lapthorn AJ, Coggins JR
Title The interaction of shikimate kinase from Erwinia chrystanthemi with substrates.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9600856
Journal J Mol Biol
Year 1998
Volume 278
Pages 983-97
Authors Krell T, Coggins JR, Lapthorn AJ
Title The three-dimensional structure of shikimate kinase.
Related PDB
Related UniProtKB P10880
[6]
Resource
Comments
Medline ID
PubMed ID 10959638
Journal J Biomol NMR
Year 2000
Volume 17
Pages 277-8
Authors Liu Q, Li Y, Wu Y, Yan H
Title Letter to the editor: 1H, 13C and 15N resonance assignments of Aquifex aeolicus shikimate kinase in complex with the substrate shikimate.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11369852
Journal Protein Sci
Year 2001
Volume 10
Pages 1137-49
Authors Krell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, Kelly SM, Price NC, Lapthorn AJ, Coggins JR
Title Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.
Related PDB 1e6c
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11717501
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 1870-1
Authors Gu Y, Reshetnikova L, Li Y, Yan H, Singh SV, Ji X
Title Crystallization and preliminary X-ray diffraction analysis of shikimate kinase from Mycobacterium tuberculosis in complex with MgADP.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11114929
Journal J Bacteriol
Year 2001
Volume 183
Pages 292-300
Authors Daugherty M, Vonstein V, Overbeek R, Osterman A
Title Archaeal shikimate kinase, a new member of the GHMP-kinase family.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11985590
Journal Eur J Biochem
Year 2002
Volume 269
Pages 2124-32
Authors Cerasoli E, Kelly SM, Coggins JR, Boam DJ, Clarke DT, Price NC
Title The refolding of type II shikimate kinase from Erwinia chrysanthemi after denaturation in urea.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 12001235
Journal Proteins
Year 2002
Volume 47
Pages 558-562
Authors Romanowski MJ, Burley SK
Title Crystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam.
Related PDB 1kag
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 12054870
Journal J Mol Biol
Year 2002
Volume 319
Pages 779-89
Authors Gu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X
Title Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.
Related PDB 1l4u 1l4y
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 15358538
Journal FEBS Lett
Year 2004
Volume 574
Pages 49-54
Authors Dhaliwal B, Nichols CE, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK
Title Crystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase.
Related PDB 1u8a
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 15583379
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 2310-9
Authors Pereira JH, de Oliveira JS, Canduri F, Dias MV, Palma MS, Basso LA, Santos DS, de Azevedo WF Jr
Title Structure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
Related PDB 1we2
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 16021622
Journal Proteins
Year 2005
Volume 60
Pages 787-96
Authors Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ
Title Structural analysis of a set of proteins resulting from a bacterial genomics project.
Related PDB 1via
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 16291688
Journal J Bacteriol
Year 2005
Volume 187
Pages 8156-63
Authors Cheng WC, Chang YN, Wang WC
Title Structural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase.
Related PDB 1zuh 1zui
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 16834327
Journal Biochemistry
Year 2006
Volume 45
Pages 8539-45
Authors Gan J, Gu Y, Li Y, Yan H, Ji X
Title Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue.
Related PDB 1zyu 2g1j 2g1k
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 17020768
Journal J Mol Biol
Year 2006
Volume 364
Pages 411-23
Authors Hartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD
Title Mechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis.
Related PDB 2iyq 2iyr 2iys 2iyt 2iyu 2iyv 2iyw 2iyx 2iyy 2iyz
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 17183161
Journal Acta Crystallogr Sect F Struct Biol Cryst Commun
Year 2007
Volume 63
Pages 1-6
Authors Dias MV, Fa?m LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF Jr
Title Effects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis.
Related PDB 2dfn 2dft
Related UniProtKB

Comments
According to the literature [12], Lys15, Arg117 and Arg136 must be catalytically important. These residues are the only positively charged residues located in the vicinity of the site where the reaction may occur and may therefore play critical roles in the stabilization of the transition state. Moreover, this paper mentioned that Asp32 assumes a different mode of interaction with Mg2+, and the number of the coordination for Mg2+ are various between the shikimate kinase from Erwinia chrysanthemi and one from Mycobacterium [12].
According to the literature [17] and [18], this enzyme catalyzes the following phosphoryl transfer reaction:
(0) Magnesium ion, which is bound to Thr15, and Asp31 through a water molecule, may stabilize the negative charge on the beta- and gamma-phosphate groups of ATP. Sidechain of Lys14 and mainchain amide groups of P-loop stabilize the negative charge on the beta-phosphate groups.
(1) Asp33 (PDB;3vaa) acts as a general base to deprotonate the acceptor group, the hydroxyl group, of shikimate.
(2) The activated hydroxyl oxygen makes a nucleophilic attack on the gamma-phosphate group of ATP. (SN2-like reaction)
(3) During the transition-state, the sidechains of Arg118 from LID domain and Lys14 may stabilize the negative charge on the transferred group, gamma-phosphate, whereas the mainchain amide groups and the sidechain of Lys14 stabilize the negative charge on the leaving group, beta-phosphate. Magnesium ion may stabilize the negative charge on both the phosphate groups.

Created Updated
2002-05-30 2012-03-12