2HK7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH MERCURY AT 2.5 ANGSTROM RESOLUTION

Authors :   J. H. Gan, P. Prabakaran, Y. J. Gu, M. Andrykovitch, Y. Li, H. H. Liu, H. Yan, X. Ji

Date :   03 Jul 06 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Shikimate Pathway, Shikimate Dehydrogenase, Drug Design, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Gan, Y. Wu, P. Prabakaran, Y. Gu, Y. Li, M. Andrykovitch, H. Liu, Y. Gong, H. Yan, X. Ji
Structural And Biochemical Analyses Of Shikimate Dehydrogenase Aroe From Aquifex Aeolicus: Implications For The Catalytic Mechanism.
Biochemistry V. 46 9513 2007
PubMed-ID: 17649975 | Reference-DOI: 10.1021/BI602601E
(for further references see the PDB file header)

Molecule 1 - SHIKIMATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.25
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-17B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AROE
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		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, 6)

No.	Name	Count	Type	Full Name
1	HG	6	Ligand/Ion	MERCURY (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:18 , HOH A:321 , HOH A:322	BINDING SITE FOR RESIDUE HG A 270
2	AC2	SOFTWARE	MET A:1	BINDING SITE FOR RESIDUE HG A 271
3	AC3	SOFTWARE	CYS A:253	BINDING SITE FOR RESIDUE HG A 272
4	AC4	SOFTWARE	HIS B:18	BINDING SITE FOR RESIDUE HG B 270
5	AC5	SOFTWARE	MET B:1	BINDING SITE FOR RESIDUE HG B 271
6	AC6	SOFTWARE	CYS B:253	BINDING SITE FOR RESIDUE HG B 272

(no "SS Bond" information available for 2HK7)

Asymmetric Unit

No.	Residues
1	Phe A:14	-	Pro A:15
2	Val A:67	-	Pro A:68
3	Phe B:14	-	Pro B:15
4	Val B:67	-	Pro B:68

(no "SAP(SNP)/Variant" information available for 2HK7)

(no "PROSITE Motif" information available for 2HK7)

(no "Exon" information available for 2HK7)

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:269
 aligned with AROE_AQUAE | O67049 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:269
                                    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_AQUAE     1 MINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEKSILVLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVVNSPEEVIDKVQVIVNTTSVGLKDKDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEKGAKLFDGLPMLLWQGIEAFKIWNGCEVPYSVAERSVRDLRG 269
               SCOP domains d2hk7a1 A:1-105 Shikimate 5-dehydrogenase AroE                                                           d2hk7a2 A:106-269 Shikimate 5-dehydrogenase AroE                                                                                                                     SCOP domains
               CATH domains 2hk7A01 A:1-104,A:235-269 Leucine Dehydrogenase, chain A, domain 1                                      ----------------------------------------------------------------------------------------------------------------------------------2hk7A01 A:1-104,A:235-269           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhh...eeee.............eehhhhhhhh...eeee....eeee.hhhhhhhhhhh.........eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhh....ee..hhhhh.....eeee.......................eeee.....hhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hk7 A   1 MINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEKSILVLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVVNSPEEVIDKVQVIVNTTSVGLKDEDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEKGAKLLDGLPMLLWQGIEAFKIWNGCEVPYSVAERSVRDLRG 269
                                    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

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with AROE_AQUAE | O67049 from UniProtKB/Swiss-Prot  Length:269

    Alignment length:268
                                    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_AQUAE     1 MINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEKSILVLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVVNSPEEVIDKVQVIVNTTSVGLKDKDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEKGAKLFDGLPMLLWQGIEAFKIWNGCEVPYSVAERSVRDLR 268
               SCOP domains d2hk7b1 B:1-105 Shikimate 5-dehydrogenase AroE                                                           d2hk7b2 B:106-268 Shikimate 5-dehydrogenase AroE                                                                                                                    SCOP domains
               CATH domains 2hk7B01 B:1-104,B:235-268 Leucine Dehydrogenase, chain A, domain 1                                      ----------------------------------------------------------------------------------------------------------------------------------2hk7B01 B:1-104,B:235-268          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee......hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh...eeee...............hhhhhhhh...eeeee..ee....hhhhhhhhhhh.........eeeee..hhhhhhhhhhhhhh..eeee...hhhhhhhhhh...eee..hhhhhh....eeee.......................eeee.....hhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hk7 B   1 MINAQTQLYGVIGFPVKHSLSPVFQNALIRYAGLNAVYLAFEINPEELKKAFEGFKALKVKGINVTVPFKEEIIPLLDYVEDTAKEIGAVNTVKFENGKAYGYNTDWIGFLKSLKSLIPEVKEKSILVLGAGGASRAVIYALVKEGAKVFLWNRTKEKAIKLAQKFPLEVVNSPEEVIDKVQVIVNTTSVGLKDEDPEIFNYDLIKKDHVVVDIIYKETKLLKKAKEKGAKLLDGLPMLLWQGIEAFKIWNGCEVPYSVAERSVRDLR 268
                                    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

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Leucine Dehydrogenase; Chain A, domain 1 (52)

Homologous Superfamily: Leucine Dehydrogenase, chain A, domain 1 (52)

Aquifex aeolicus. Organism_taxid: 63363. (3)

1a	2hk7A01	A:1-104,A:235-269
1b	2hk7B01	B:1-104,B:235-268

(no "Pfam Domain" information available for 2HK7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (AROE_AQUAE | O67049)

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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	Cis Peptide Bonds
		Phe A:14 - Pro A:15	[ RasMol ]
		Phe B:14 - Pro B:15	[ RasMol ]
		Val A:67 - Pro A:68	[ RasMol ]
		Val B:67 - Pro B:68	[ RasMol ]

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	2hk7
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	AROE_AQUAE \| O67049
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	1.1.1.25
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	AROE_AQUAE \| O67049	:	2hk8 2hk9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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