2SHK - JenaLib

Title :   THE THREE-DIMENSIONAL STRUCTURE OF SHIKIMATE KINASE FROM ERWINIA CHRYSANTHEMI COMPLEXED WITH ADP

Authors :   T. Krell, J. R. Coggins, A. J. Lapthorn

Date :   27 Oct 97 (Deposition) - 18 Nov 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A (1x),B (1x)

Keywords :   Shikimate Kinase, Phosphoryl Transfer, Adp, Shikimate Pathway, P-Loop Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Krell, J. E. Coyle, M. J. Horsburgh, J. R. Coggins, A. J. Lapthorn
Crystallization And Preliminary X-Ray Crystallographic Analysis Of Shikimate Kinase From Erwinia Chrysanthemi.
Acta Crystallogr. , Sect. D V. 53 612 1997
PubMed-ID: 15299895 | Reference-DOI: 10.1107/S0907444997004319
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:912 , GLN B:144 , ALA B:147 , HOH B:924 , HOH B:967	BINDING SITE FOR RESIDUE MG B 901
2	AC2	SOFTWARE	GLN A:144 , ALA A:147 , HOH A:904 , HOH A:946 , HOH B:913	BINDING SITE FOR RESIDUE MG A 902
3	AC3	SOFTWARE	ARG A:92 , ALA A:93 , GLY A:95 , ARG B:92 , HIS B:94 , GLY B:95	BINDING SITE FOR RESIDUE MG A 903
4	AC4	SOFTWARE	THR B:16 , ASP B:32 , ADP B:905 , HOH B:958	BINDING SITE FOR RESIDUE MG B 904
5	AC5	SOFTWARE	ALA B:10 , GLY B:12 , CYS B:13 , GLY B:14 , LYS B:15 , THR B:16 , THR B:17 , ARG B:110 , ALA B:153 , GLN B:155 , PRO B:156 , PRO B:157 , ILE B:160 , MG B:904 , HOH B:915	BINDING SITE FOR RESIDUE ADP B 905
6	PIP	UNKNOWN	GLY B:9 , GLY B:14 , LYS B:15 , THR B:16	A WALKER TYPE-A MOTIF FORMS THE P-LOOP WHICH IS THE BINDING SITE FOR THE PHOSPHATES OF ATP.
7	POP	UNKNOWN	GLY A:9 , GLY A:14 , LYS A:15 , THR A:16	A WALKER TYPE-A MOTIF FORMS THE P-LOOP WHICH IS THE BINDING SITE FOR THE PHOSPHATES OF ATP.
8	SAS	UNKNOWN	ASP A:34 , GLU A:61 , ARG A:58 , ARG A:139	THE ELECTRON DENSITY FOR SHIKIMATE WAS AMBIGUOUS PREVENTING ITS INCLUSION IN THE MODEL. THE LISTED RESIDUES ARE GROUPED AROUND THE DENSITY AND ARE MOST LIKELY TO BE PART OF THE SHIKIMATE-BINDING SITE. ALL RESIDUES ARE CONSERVED IN A SEQUENCE ALIGNMENT OF SHIKIMATE KINASES.
9	SBS	UNKNOWN	ASP B:34 , GLU B:61 , ARG B:58 , ARG B:139	THE ELECTRON DENSITY FOR SHIKIMATE WAS AMBIGUOUS PREVENTING ITS INCLUSION IN THE MODEL. THE LISTED RESIDUES ARE GROUPED AROUND THE DENSITY AND ARE MOST LIKELY TO BE PART OF THE SHIKIMATE-BINDING SITE. ALL RESIDUES ARE CONSERVED IN A SEQUENCE ALIGNMENT OF SHIKIMATE KINASES.

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:158
 aligned with AROL_DICCH | P10880 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:173
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
           AROL_DICCH     1 MTEPIFMVGARGCGKTTVGRELARALGYEFVDTDIFMQHTSGMTVADVVAAEGWPGFRRRESEALQAVATPNRVVATGGGMVLLEQNRQFMRAHGTVVYLFAPAEELALRLQASPQAHQRPTLTGRPIAEEMEAVLREREALYQDVAHYVVDATQPPAAIVCELMQTMRLPAA 173
               SCOP domains d2shka_ A: Shikimate kinase (AroK)                                                                                                                                            SCOP domains
               CATH domains 2shkA00 A:1-173 P-loop containing nucleotide triphosphate hydrolases                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhh..eeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhheeeeeee..hhhhhh...---------------.hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------SHIKIMATE_KINASE         ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2shk A   1 MTEPIFMVGARGCGKTTVGRELARALGYEFVDTDIFMQHTSGMTVADVVAAEGWPGFRRRESEALQAVATPNRVVATGGGMVLLEQNRQFMRAHGTVVYLFAPAEELALRLQ---------------IAEEMEAVLREREALYQDVAHYVVDATQPPAAIVCELMQTMRLPAA 173
                                    10        20        30        40        50        60        70        80        90       100       110 |       -       130       140       150       160       170   
                                                                                                                                         112             128

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with AROL_DICCH | P10880 from UniProtKB/Swiss-Prot  Length:173

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
           AROL_DICCH     1 MTEPIFMVGARGCGKTTVGRELARALGYEFVDTDIFMQHTSGMTVADVVAAEGWPGFRRRESEALQAVATPNRVVATGGGMVLLEQNRQFMRAHGTVVYLFAPAEELALRLQASPQAHQRPTLTGRPIAEEMEAVLREREALYQDVAHYVVDATQPPAAIVCELMQTMRLPA 172
               SCOP domains d2shkb_ B: Shikimate kinase (AroK)                                                                                                                                           SCOP domains
               CATH domains 2shkB00 B:1-172 P-loop containing nucleotide triphosphate hydrolases                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhh..eeeehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhh.hhhhhhhh..eeeeeee..hhhhhh...----------.....hhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------SHIKIMATE_KINASE         ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2shk B   1 MTEPIFMVGARGCGKTTVGRELARALGYEFVDTDIFMQHTSGMTVADVVAAEGWPGFRRRESEALQAVATPNRVVATGGGMVLLEQNRQFMRAHGTVVYLFAPAEELALRLQ----------LTGRPIAEEMEAVLREREALYQDVAHYVVDATQPPAAIVCELMQTMRLPA 172
                                    10        20        30        40        50        60        70        80        90       100       110 |       -  |    130       140       150       160       170  
                                                                                                                                         112        123

Legend:		→ Mismatch	(orange background)
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	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, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AROL_DICCH | P10880)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0004765	shikimate kinase activity	Catalysis of the reaction: ATP + shikimate = 3-phosphoshikimate + ADP + 2 H(+).
	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:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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