EzCatDB: S00304
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DB codeS00304
RLCP classification3.103.70035.360 : Transfer
CATH domainDomain 13.40.50.300 : Rossmann foldCatalytic domain
E.C.2.7.1.71

CATH domainRelated DB codes (homologues)
3.40.50.300 : Rossmann foldS00527,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

Enzyme Name
UniProtKBKEGG

P10880Q83AJ3Q8A2B2
Protein nameShikimate kinase 2Shikimate kinaseShikimate kinaseshikimate kinase
shikimate kinase (phosphorylating)
shikimate kinase II
SynonymsSK 2
EC 2.7.1.71
Shikimate kinase II
SKII
SK
EC 2.7.1.71
SK
EC 2.7.1.71
RefSeq
NP_820869.1 (Protein)
NC_002971.3 (DNA/RNA sequence)
NP_812305.1 (Protein)
NC_004663.1 (DNA/RNA sequence)
PfamPF01202 (SKI)
[Graphical view]
PF01202 (SKI)
[Graphical view]
PF01202 (SKI)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00400Phenylalanine, tyrosine and tryptophan biosynthesis

UniProtKB:Accession NumberP10880Q83AJ3Q8A2B2
Entry nameAROL_ERWCHAROK_COXBUAROK_BACTN
ActivityATP + shikimate = ADP + shikimate 3-phosphate.ATP + shikimate = ADP + shikimate 3-phosphate.ATP + shikimate = ADP + shikimate 3-phosphate.
SubunitMonomer.Monomer (By similarity).Monomer (By similarity).
Subcellular locationCytoplasm (Probable).Cytoplasm (Probable).Cytoplasm (Probable).
CofactorBinds 1 magnesium ion per subunit.Binds 1 magnesium ion per subunit (By similarity).Binds 1 magnesium ion per subunit (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00493C00008C03175
CompoundmagnesiumATPShikimateADPShikimate 3-phosphate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,carboxyl groupamine group,nucleotidecarbohydrate,carboxyl group,phosphate group/phosphate ion
ChEBI18420
15422
16119
16761
17052
PubChem888
5957
8742
6022
121947
             
1e6cAUnboundUnboundUnboundUnboundUnbound
1e6cBUnboundUnboundUnboundUnboundUnbound
1shkAUnboundUnboundUnboundUnboundUnbound
1shkBUnboundUnboundUnboundUnboundUnbound
2shkAUnboundUnboundUnboundUnboundUnbound
2shkBBound:_MG 903UnboundUnboundBound:ADPUnbound
3trfAUnboundUnboundUnboundUnboundUnbound
3trfBUnboundUnboundUnboundUnboundUnbound
3vaaAUnboundUnboundUnboundUnboundUnbound
3vaaBUnboundUnboundUnboundUnboundUnbound
3vaaCUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [12]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
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
1shkALYS 15;ASP 34;       
THR 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;THR 16
invisible 113-127
1shkBLYS 15;ASP 34;       
THR 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;THR 16
invisible 113-125
2shkALYS 15;ASP 34;       
THR 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;THR 16
invisible 113-127
2shkBLYS 15;ASP 34;       
THR 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;THR 16
invisible 113-122
3trfALYS 18;ASP 37;ARG 123
THR 19;ASP 35(Mg2+ binding)
GLY 15;GLY 17;LYS 18;THR 19
 
3trfBLYS 18;ASP 37;ARG 123
THR 19;ASP 35(Mg2+ binding)
GLY 15;GLY 17;LYS 18;THR 19
 
3vaaALYS 14;ASP 33;ARG 118
THR 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;THR 15
 
3vaaBLYS 14;ASP 33;ARG 118
THR 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;THR 15
 
3vaaCLYS 14;ASP 33;       
THR 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;THR 15
invisible 114-120

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]p.991
[12]p.784
[17]p.8541-8542
[18]p.417-419

references
[1]
PubMed ID1849480
JournalEur J Biochem
Year1991
Volume196
Pages717-24
AuthorsHawkins AR, Smith M
TitleDomain structure and interaction within the pentafunctional arom polypeptide.
[2]
PubMed ID8682786
JournalJ Bacteriol
Year1996
Volume178
Pages3818-28
AuthorsVinella D, Gagny B, Joseleau-Petit D, D'Ari R, Cashel M
TitleMecillinam resistance in Escherichia coli is conferred by loss of a second activity of the AroK protein.
[3]
JournalActa Crystallogr D Biol Crystallogr
Year1997
Volume53
Pages612-614
AuthorsKrell T, Coyle JE, Horsburgh MJ, Coggins JR, Lapthorn AJ
TitleCrystallization and preliminary x-ray crystallographic analysis of shikimate kinase.
Related PDB1shk,2shk
[4]
PubMed ID9450055
JournalBiochem Soc Trans
Year1997
Volume25
PagesS627
AuthorsIdziak C, Price NC, Kelly SM, Krell T, Boam DJ, Lapthorn AJ, Coggins JR
TitleThe interaction of shikimate kinase from Erwinia chrystanthemi with substrates.
[5]
PubMed ID9600856
JournalJ Mol Biol
Year1998
Volume278
Pages983-97
AuthorsKrell T, Coggins JR, Lapthorn AJ
TitleThe three-dimensional structure of shikimate kinase.
Related UniProtKBP10880
[6]
PubMed ID10959638
JournalJ Biomol NMR
Year2000
Volume17
Pages277-8
AuthorsLiu Q, Li Y, Wu Y, Yan H
TitleLetter to the editor: 1H, 13C and 15N resonance assignments of Aquifex aeolicus shikimate kinase in complex with the substrate shikimate.
[7]
PubMed ID11369852
JournalProtein Sci
Year2001
Volume10
Pages1137-49
AuthorsKrell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, Kelly SM, Price NC, Lapthorn AJ, Coggins JR
TitleBiochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.
Related PDB1e6c
[8]
PubMed ID11717501
JournalActa Crystallogr D Biol Crystallogr
Year2001
Volume57
Pages1870-1
AuthorsGu Y, Reshetnikova L, Li Y, Yan H, Singh SV, Ji X
TitleCrystallization and preliminary X-ray diffraction analysis of shikimate kinase from Mycobacterium tuberculosis in complex with MgADP.
[9]
PubMed ID11114929
JournalJ Bacteriol
Year2001
Volume183
Pages292-300
AuthorsDaugherty M, Vonstein V, Overbeek R, Osterman A
TitleArchaeal shikimate kinase, a new member of the GHMP-kinase family.
[10]
PubMed ID11985590
JournalEur J Biochem
Year2002
Volume269
Pages2124-32
AuthorsCerasoli E, Kelly SM, Coggins JR, Boam DJ, Clarke DT, Price NC
TitleThe refolding of type II shikimate kinase from Erwinia chrysanthemi after denaturation in urea.
[11]
PubMed ID12001235
JournalProteins
Year2002
Volume47
Pages558-562
AuthorsRomanowski MJ, Burley SK
TitleCrystal structure of the Escherichia coli shikimate kinase I (AroK) that confers sensitivity to mecillinam.
Related PDB1kag
[12]
PubMed ID12054870
JournalJ Mol Biol
Year2002
Volume319
Pages779-89
AuthorsGu Y, Reshetnikova L, Li Y, Wu Y, Yan H, Singh S, Ji X
TitleCrystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis.
Related PDB1l4u,1l4y
[13]
PubMed ID15358538
JournalFEBS Lett
Year2004
Volume574
Pages49-54
AuthorsDhaliwal B, Nichols CE, Ren J, Lockyer M, Charles I, Hawkins AR, Stammers DK
TitleCrystallographic studies of shikimate binding and induced conformational changes in Mycobacterium tuberculosis shikimate kinase.
Related PDB1u8a
[14]
PubMed ID15583379
JournalActa Crystallogr D Biol Crystallogr
Year2004
Volume60
Pages2310-9
AuthorsPereira JH, de Oliveira JS, Canduri F, Dias MV, Palma MS, Basso LA, Santos DS, de Azevedo WF Jr
TitleStructure of shikimate kinase from Mycobacterium tuberculosis reveals the binding of shikimic acid.
Related PDB1we2
[15]
PubMed ID16021622
JournalProteins
Year2005
Volume60
Pages787-96
AuthorsBadger 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
TitleStructural analysis of a set of proteins resulting from a bacterial genomics project.
Related PDB1via
[16]
PubMed ID16291688
JournalJ Bacteriol
Year2005
Volume187
Pages8156-63
AuthorsCheng WC, Chang YN, Wang WC
TitleStructural basis for shikimate-binding specificity of Helicobacter pylori shikimate kinase.
Related PDB1zuh,1zui
[17]
PubMed ID16834327
JournalBiochemistry
Year2006
Volume45
Pages8539-45
AuthorsGan J, Gu Y, Li Y, Yan H, Ji X
TitleCrystal structure of Mycobacterium tuberculosis shikimate kinase in complex with shikimic acid and an ATP analogue.
Related PDB1zyu,2g1j,2g1k
[18]
PubMed ID17020768
JournalJ Mol Biol
Year2006
Volume364
Pages411-23
AuthorsHartmann MD, Bourenkov GP, Oberschall A, Strizhov N, Bartunik HD
TitleMechanism of phosphoryl transfer catalyzed by shikimate kinase from Mycobacterium tuberculosis.
Related PDB2iyq,2iyr,2iys,2iyt,2iyu,2iyv,2iyw,2iyx,2iyy,2iyz
[19]
PubMed ID17183161
JournalActa Crystallogr Sect F Struct Biol Cryst Commun
Year2007
Volume63
Pages1-6
AuthorsDias MV, Fa?m LM, Vasconcelos IB, de Oliveira JS, Basso LA, Santos DS, de Azevedo WF Jr
TitleEffects of the magnesium and chloride ions and shikimate on the structure of shikimate kinase from Mycobacterium tuberculosis.
Related PDB2dfn,2dft

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.

createdupdated
2002-05-302012-03-12


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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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