3HR7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE SHIKIMATE KINASE-SULFATE COMPLEX FROM HELICOBACTER PYLORI

Authors :   W. C. Cheng, W. C. Wang

Date :   09 Jun 09 (Deposition) - 16 Jun 10 (Release) - 30 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Three-Layer Alpha/Beta Fold, Nucleoside Monophosphate (Nmp) Kinase Family, Amino-Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Atp-Binding, Kinase, Magnesium, Metal-Binding, Nucleotide-Binding, 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
(for further references see the PDB file header)

Molecule 1 - SHIKIMATE KINASE
	Chains	:	A, B
	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
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695
	Synonym	:	SK

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:11 , SER A:12 , GLY A:13 , LYS A:14 , SER A:15 , HOH A:222	BINDING SITE FOR RESIDUE SO4 A 202
2	AC2	SOFTWARE	PHE B:9 , GLY B:11 , SER B:12 , GLY B:13 , LYS B:14 , SER B:15 , HOH B:207 , HOH B:223 , HOH B:231 , HOH B:268 , HOH B:316	BINDING SITE FOR RESIDUE SO4 B 202

(no "SS Bond" information available for 3HR7)

(no "Cis Peptide Bond" information available for 3HR7)

(no "SAP(SNP)/Variant" information available for 3HR7)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SHIKIMATE_KINASE	PS01128	Shikimate kinase signature.	AROK_HELPY	57-83	2	A:57-83 B:57-83

(no "Exon" information available for 3HR7)

Asymmetric/Biological 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:151
 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 3hr7A00 A:1-162 P-loop containing nucleotide triphosphate hydrolases                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhh......eeeeeee.hhhhhhhh-----------.....hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE           ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hr7 A   1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKR-----------LNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIA 162
                                    10        20        30        40        50        60        70        80        90       100      |  -       120       130       140       150       160  
                                                                                                                                    107         119

Chain B from PDB  Type:PROTEIN  Length:155
 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 3hr7B00 B:1-162 P-loop containing nucleotide triphosphate hydrolases                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhh..eeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee...hhhhh..hhh.eeeeeee.hhhhhhhhhh.-------....hhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------SHIKIMATE_KINASE           ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hr7 B   1 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDTDMIISERVGLSVREIFEELGEDNFRMFEKNLIDELKTLKTPHVISTGGGIVMHENLKGLGTTFYLKMDFETLIKRLNQ-------LLNNLTQAKELFEKRQALYEKNASFIIDARGGLNNSLKQVLQFIA 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
                                                                                                                                       110     118

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 3HR7)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Helicobacter pylori. Organism_taxid: 85962. Strain: 26695. (1)

1a	3hr7B00	B:1-162
1b	3hr7A00	A:1-162

(no "Pfam Domain" information available for 3HR7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hr7)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3hr7
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	AROK_HELPY \| P56073
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.71
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	AROK_HELPY \| P56073
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	AROK_HELPY \| P56073	:	1zuh 1zui 3mrs 3muf 3n2e

1zuh	THE APO FORM OF THE SAME PROTEIN.
1zui	THE SAME PROTEIN COMPLEXED WITH SHIKIMATE AND PHOSPHATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File