EzCatDB: S00554
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DB codeS00554
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,S00555,S00671,S00672,S00676,S00680,S00682,S00913,S00914,S00301,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00129,D00130,D00540,M00186

Enzyme Name
UniProtKBKEGG

P0A6D7P0A4Z2P56073Q0PBC3
Protein nameShikimate kinase 1Shikimate kinaseShikimate kinase
shikimate kinase
shikimate kinase (phosphorylating)
shikimate kinase II
SynonymsSK 1
EC 2.7.1.71
Shikimate kinase I
SKI
SK
EC 2.7.1.71
SK
EC 2.7.1.71
Shikimate kinase
EC 2.7.1.71
RefSeqYP_026215.2 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492042.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_217055.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_337110.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006515980.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
NP_206956.1 (Protein)
NC_000915.1 (DNA/RNA sequence)
YP_006934081.1 (Protein)
NC_018939.1 (DNA/RNA sequence)
YP_002343824.1 (Protein)
NC_002163.1 (DNA/RNA sequence)
PfamPF01202 (SKI)
[Graphical view]
PF01202 (SKI)
[Graphical view]
PF01202 (SKI)
[Graphical view]
PF01202 (SKI)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00400Phenylalanine, tyrosine and tryptophan biosynthesis

UniProtKB:Accession NumberP0A6D7P0A4Z2P56073Q0PBC3
Entry nameAROK_ECOLIAROK_MYCTUAROK_HELPYQ0PBC3_CAMJE
ActivityATP + shikimate = ADP + shikimate 3-phosphate.ATP + shikimate = ADP + shikimate 3-phosphate.ATP + shikimate = ADP + shikimate 3-phosphate.ATP + shikimate = ADP + shikimate 3-phosphate.
SubunitMonomer.Monomer.Monomer (By similarity).Monomer (By similarity).
Subcellular locationCytoplasm (Probable).Cytoplasm (Probable).Cytoplasm (Probable).Cytoplasm (By similarity).
CofactorBinds 1 magnesium ion per subunit (Probable).Binds 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
             
1kagAUnboundUnboundUnboundUnboundUnbound
1kagBUnboundUnboundUnboundUnboundUnbound
1l4uABound:_MGUnboundUnboundBound:ADPUnbound
1l4yABound:_MGUnboundUnboundBound:ADPUnbound
1u8aAUnboundUnboundBound:SKMBound:ADPUnbound
1we2ABound:_MGUnboundAnalogue:DHKBound:ADPUnbound
1zyuAUnboundAnalogue:ACPBound:SKMUnboundUnbound
2dfnAUnboundUnboundBound:SKMBound:ADPUnbound
2dftABound:_MGUnboundUnboundBound:ADPUnbound
2dftBBound:_MGUnboundUnboundBound:ADPUnbound
2dftCBound:_MGUnboundUnboundBound:ADPUnbound
2dftDBound:_MGUnboundUnboundBound:ADPUnbound
2g1jAUnboundUnboundUnboundUnboundUnbound
2g1jBUnboundUnboundUnboundUnboundUnbound
2g1kAUnboundUnboundBound:SKMUnboundUnbound
2iyqAUnboundUnboundBound:SKMBound:ADPUnbound
2iyrAUnboundUnboundBound:SKMUnboundUnbound
2iyrBUnboundUnboundBound:SKMUnboundUnbound
2iysAUnboundUnboundBound:SKMUnboundUnbound
2iytAUnboundUnboundUnboundUnboundUnbound
2iyuAUnboundUnboundUnboundBound:ADPUnbound
2iyvAUnboundUnboundUnboundBound:ADPUnbound
2iywABound:_MGBound:ATPUnboundUnboundUnbound
2iyxAUnboundUnboundBound:SKMUnboundUnbound
2iyyAUnboundUnboundUnboundUnboundBound:S3P
2iyzAUnboundUnboundUnboundBound:ADPBound:S3P
3bafAUnboundAnalogue:ANPBound:SKMUnboundUnbound
1zuhAUnboundUnboundUnboundUnboundUnbound
1zuiAUnboundUnboundBound:SKMUnboundUnbound
3hr7AUnboundUnboundUnboundUnboundUnbound
3hr7BUnboundUnboundUnboundUnboundUnbound
3mrsAUnboundUnboundUnboundUnboundUnbound
3mufAUnboundUnboundUnboundBound:ADPBound:S3P
3n2eAUnboundUnboundUnboundUnboundUnbound
3n2eBUnboundUnboundUnboundUnboundUnbound
3n2eCUnboundUnboundUnboundUnboundUnbound
1viaAUnboundUnboundUnboundUnboundUnbound
1viaBUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [12]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1kagALYS 17;ASP 36;       
SER 18;ASP 34(Mg2+ binding)
GLY 14;GLY 16;LYS 17;SER 18
invisible 115-120, 153-157
1kagBLYS 17;ASP 36;       
SER 18;ASP 34(Mg2+ binding)
GLY 14;GLY 16;LYS 17;SER 18
invisible 113-127, 153-158
1l4uALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
1l4yALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
1u8aALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 114-115
1we2ALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
1zyuALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2dfnALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2dftALYS 15;ASP 34;       
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 115-123
2dftBLYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2dftCLYS 15;ASP 34;       
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 114-123
2dftDLYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2g1jALYS 15;ASP 34;       
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 114-120
2g1jBLYS 15;ASP 34;       
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 114-120
2g1kALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyqALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyrALYS 15;ASP 34;       
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 116-120
2iyrBLYS 15;ASP 34;       
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 117-118
2iysALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iytALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyuALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyvALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iywALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyxALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyyALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
2iyzALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
invisible 152
3bafALYS 15;ASP 34;ARG 117
SER 16;ASP 32(Mg2+ binding)
GLY 12;GLY 14;LYS 15;SER 16
 
1zuhALYS 14;ASP 33;       
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
invisible 111-118
1zuiALYS 14;ASP 33;ARG 116
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
invisible 111-112
3hr7ALYS 14;ASP 33;       
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
invisible 108-118
3hr7BLYS 14;ASP 33;       
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
invisible 111-117
3mrsALYS 14;ASP 33;       
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
invisible 109-121, mutant R57A
3mufALYS 14;ASP 33;ARG 116
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
 
3n2eALYS 14;ASP 33;ARG 116
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
 
3n2eBLYS 14;ASP 33;ARG 116
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
 
3n2eCLYS 14;ASP 33;       
SER 15;ASP 31(Mg2+ binding)
GLY 11;GLY 13;LYS 14;SER 15
invisible 101-133
1viaALYS 17;ASP 36;ARG 118
SER 18;ASP 34(Mg2+ binding)
GLY 14;GLY 16;LYS 17;SER 18
 
1viaBLYS 17;ASP 36;       
SER 18;ASP 34(Mg2+ binding)
GLY 14;GLY 16;LYS 17;SER 18
invisible 111-121

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
This enzyme is homologous to those from other bacteria (S00304, S00555 in EzCatDB), but has got a slightly different catalytic site.
According to the literature [17] and [18], this enzyme catalyzes the following phosphoryl transfer reaction:
(0) Magnesium ion, which is bound to Ser16, and Asp32 through a water molecule, may stabilize the negative charge on the beta- and gamma-phosphate groups of ATP. Sidechain of Lys15 and mainchain amide groups of P-loop stabilize the negative charge on the beta-phosphate groups.
(1) Asp34 (PDB;1l4u) 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 Arg117 from LID domain and Lys15 may stabilize the negative charge on the transferred group, gamma-phosphate, whereas the mainchain amide groups and the sidechain of Lys15 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


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
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)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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