3PHJ - JenaLib

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Title :   SHIKIMATE 5-DEHYDROGENASE (AROE) FROM HELICOBACTER PYLORI IN COMPLEX WITH 3-DEHYDROSHIKIMATE

Authors :   W. C. Cheng, S. C. Lin, C. H. Lin, W. C. Wang

Date :   04 Nov 10 (Deposition) - 09 Nov 11 (Release) - 09 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Shikimate Dehydrogenase, Shikimate Pathway, Helicobacter Pylori, Oxidoreductase, Alpha/Beta Domain, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. C. Cheng, S. C. Lin, C. H. Lin, W. C. Wang
Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori I Complex With 3-Dehydroshikimate
To Be Published
PubMed: search

Molecule 1 - SHIKIMATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AROE, HP_1249
	Organism Common	:	CAMPYLOBACTER PYLORI
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	DHK	2	Ligand/Ion	3-DEHYDROSHIKIMATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	DHK	1	Ligand/Ion	3-DEHYDROSHIKIMATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	DHK	1	Ligand/Ion	3-DEHYDROSHIKIMATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:16 , SER A:18 , ASN A:63 , LYS A:69 , ASN A:90 , ASP A:105 , TYR A:210 , GLN A:237	BINDING SITE FOR RESIDUE DHK A 500
2	AC2	SOFTWARE	SER B:16 , SER B:18 , ASN B:63 , THR B:65 , LYS B:69 , ASN B:90 , ASP B:105 , TYR B:210 , GLN B:237	BINDING SITE FOR RESIDUE DHK B 500

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

Asymmetric Unit

No.	Residues
1	Asn A:11	-	Pro A:12
2	Leu A:66	-	Pro A:67
3	Asn B:11	-	Pro B:12
4	Leu B:66	-	Pro B:67

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

(no "PROSITE Motif" information available for 3PHJ)

(no "Exon" information available for 3PHJ)

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:255
 aligned with AROE_HELPY | P56119 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
           AROE_HELPY     1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQKNYQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
               SCOP domains d3phja1 A:1-104 automated matches                                                                       d3phja2 A:   105-263 automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhh...eeee...hhhhhhhhh.ee..hhhhhh...eeeee..eeeee.hhhhhhhhhh.---..eeeee..hhhhhhhhhhhhhh..eeeee.....hhhhhhhhh.eee.........eeee...-----....hhhhhhhhhhhh.eeee......hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3phj A   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLK---YQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATS-----ELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180|     |190       200       210       220       230       240       250       260   
                                                                                                                                           114 118                                                            181   187

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with AROE_HELPY | P56119 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
           AROE_HELPY     1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQKNYQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
               SCOP domains d3phjb1 B:1-104 automated matches                                                                       d3phjb2 B:   105-263 automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeee......hhhhhhhh.eeeeee...hhhhhhhhh.ee..hhhhhh...eeeee..eeeee.hhhhhhhhh..---..eeeee..hhhhhhhhhhhhhh..eeeee.....hhhhhhhh..eee.........eeee...-----....hhhhhhhhhhhh.eeee......hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3phj B   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLK---YQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATS-----ELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180|     |190       200       210       220       230       240       250       260   
                                                                                                                                           114 118                                                            181   187

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 "CATH Domain" information available for 3PHJ)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (AROE_HELPY | P56119)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0004764	shikimate 3-dehydrogenase (NADP+) activity	Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0019632	shikimate metabolic process	The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.

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

	Cis Peptide Bonds
		Asn A:11 - Pro A:12	[ RasMol ]
		Asn B:11 - Pro B:12	[ RasMol ]
		Leu A:66 - Pro A:67	[ RasMol ]
		Leu B:66 - Pro B:67	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3phj
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	AROE_HELPY \| P56119
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	1.1.1.25
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		Disease Information	:	OMIM

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	AROE_HELPY \| P56119
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UniProtKB/Swiss-Prot
	AROE_HELPY \| P56119	:	3phg 3phh 3phi 4foo 4fos 4fpx 4fq8 4fr5 4fsh

3phg	THE APO FORM OF THE SAME PROTEIN
3phh	THE SAME PROTEIN COMPLEXED WITH SHIKIMATE
3phi	THE SAME PROTEIN COMPLEXED WITH SHIKIMATE AND NADPH

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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