3N2E - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HELICOBACTOR PYLORI SHIKIMATE KINASE IN COMPLEX WITH NSC162535

Authors :   W. C. Cheng, T. J. Chen, S. C. Lin, W. C. Wang

Date :   18 May 10 (Deposition) - 18 May 11 (Release) - 30 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.53

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Alpha-Beta-Alpha Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. C. Cheng, Y. F. Chen, H. J. Wang, K. C. Hsu, S. C. Lin, T. J. Chen, J. M. Yang, W. C. Wang
Structures Of Helicobacter Pylori Shikimate Kinase Reveal A Selective Inhibitor-Induced-Fit Mechanism
Plos One V. 7 33481 2012
PubMed-ID: 22438938 | Reference-DOI: 10.1371/JOURNAL.PONE.0033481

Molecule 1 - SHIKIMATE KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.1.71
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AROK
	Mutation	:	YES
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695
	Synonym	:	SK

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	OSA	2	Ligand/Ion	7-AMINO-4-HYDROXY-3-[(E)-(5-HYDROXY-7-SULFONAPHTHALEN-2-YL)DIAZENYL]NAPHTHALENE-2-SULFONIC ACID
2	TLA	5	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	OSA	1	Ligand/Ion	7-AMINO-4-HYDROXY-3-[(E)-(5-HYDROXY-7-SULFONAPHTHALEN-2-YL)DIAZENYL]NAPHTHALENE-2-SULFONIC ACID
2	TLA	2	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	OSA	1	Ligand/Ion	7-AMINO-4-HYDROXY-3-[(E)-(5-HYDROXY-7-SULFONAPHTHALEN-2-YL)DIAZENYL]NAPHTHALENE-2-SULFONIC ACID
2	TLA	3	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	OSA	-1	Ligand/Ion	7-AMINO-4-HYDROXY-3-[(E)-(5-HYDROXY-7-SULFONAPHTHALEN-2-YL)DIAZENYL]NAPHTHALENE-2-SULFONIC ACID
2	TLA	-1	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:9 , MET A:10 , ARG A:45 , PHE A:48 , GLU A:53 , ARG A:57 , GLY A:80 , GLY A:81 , VAL A:83 , MET A:84 , ARG A:116 , ARG A:132 , LEU A:135 , TYR A:136 , HOH A:179 , HOH A:201 , TLA A:2001 , TLA A:2002	BINDING SITE FOR RESIDUE OSA A 1001
2	AC2	SOFTWARE	GLU A:53 , ARG A:116 , LEU A:118 , ARG A:132 , HOH A:184 , OSA A:1001	BINDING SITE FOR RESIDUE TLA A 2001
3	AC3	SOFTWARE	PHE A:9 , PHE A:101 , ILE A:105 , ARG A:116 , LEU A:119 , ALA A:125 , LEU A:128 , PHE A:129 , ARG A:132 , OSA A:1001	BINDING SITE FOR RESIDUE TLA A 2002
4	AC4	SOFTWARE	PHE B:9 , MET B:10 , ARG B:45 , PHE B:48 , GLU B:53 , ARG B:57 , GLY B:80 , VAL B:83 , MET B:84 , ARG B:116 , ARG B:132 , LEU B:135 , TYR B:136 , HOH B:170 , HOH B:187 , TLA B:2001 , TLA B:2003	BINDING SITE FOR RESIDUE OSA B 1001
5	AC5	SOFTWARE	GLU B:53 , ARG B:116 , ARG B:132 , HOH B:172 , OSA B:1001	BINDING SITE FOR RESIDUE TLA B 2001
6	AC6	SOFTWARE	MET B:10 , GLY B:11 , SER B:12 , GLY B:13 , LYS B:14 , SER B:15 , ASP B:31 , HOH B:198	BINDING SITE FOR RESIDUE TLA B 2002
7	AC7	SOFTWARE	PHE B:9 , MET B:10 , LEU B:104 , ILE B:105 , ARG B:116 , ALA B:125 , LEU B:128 , ARG B:132 , OSA B:1001	BINDING SITE FOR RESIDUE TLA B 2003

(no "SS Bond" information available for 3N2E)

(no "Cis Peptide Bond" information available for 3N2E)

(no "SAP(SNP)/Variant" information available for 3N2E)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_HELPY	57-83	3	A:57-83 B:57-83 C:57-83

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_HELPY	57-83	1	A:57-83 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_HELPY	57-83	1	- B:57-83 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_HELPY	57-83	1	- - C:57-83

(no "Exon" information available for 3N2E)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:168
 aligned with AROK_HELPY | P56073 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:168
                                                                                                                                                                                           162      
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 |      
           AROK_HELPY     1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKEREKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIA------   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE           ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n2e A   1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKERAKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIALQPSLS 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain B from PDB  Type:PROTEIN  Length:162
 aligned with AROK_HELPY | P56073 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           AROK_HELPY     1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKEREKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIA 162
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE           ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3n2e B   1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKERAKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIA 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain C from PDB  Type:PROTEIN  Length:134
 aligned with AROK_HELPY | P56073 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:167
                                                                                                                                                                                           162     
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 |     
           AROK_HELPY     1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQKEREKRPLLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIA-----   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------SKI-3n2eC01 C:10-162                                                                                                                                     ----- Pfam domains (1)
           Pfam domains (2) ---------SKI-3n2eC02 C:10-162                                                                                                                                     ----- Pfam domains (2)
           Pfam domains (3) ---------SKI-3n2eC03 C:10-162                                                                                                                                     ----- Pfam domains (3)
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhh......eeeeeee..---------------------------------hhhhhhh.eeee...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE           ------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n2e C   1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMD---------------------------------ALYEKNASFIIDARGGLNNSLKQVLQFIALQPSL 167
                                    10        20        30        40        50        60        70        80        90       100         -         -         -   |   140       150       160       
                                                                                                                             100                               134

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

(no "SCOP Domain" information available for 3N2E)

(no "CATH Domain" information available for 3N2E)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: SKI (16)

Helicobacter pylori (Campylobacter pylori) (5)

1a	SKI-3n2eC01	C:10-162
1b	SKI-3n2eC02	C:10-162
1c	SKI-3n2eC03	C:10-162

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (AROK_HELPY | P56073)

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.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Units
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Access by PDB/NDB ID
	3n2e
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	AROK_HELPY \| P56073
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	2.7.1.71
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	AROK_HELPY \| P56073
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UniProtKB/Swiss-Prot
	AROK_HELPY \| P56073	:	1zuh 1zui 3hr7 3mrs 3muf

1zuh	THE SAME PROTEIN OF APO FORM.
1zui	THE SAME PROTEIN COMPLEXED WITH SHIKIMATE.
3hr7	THE SAME PROTEIN OF DIMERIC FORM.
3mrs	THE SAME PROTEIN OF R57A MUTANT.
3muf	THE SAME PROTEIN COMPLEXED WITH SHIKIMATE-3-PHOSPHATE AND ADP.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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SCOP Domains (0, 0)

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Pfam Domains (1, 3)

Gene Ontology (12, 12)

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