2YSW - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE 3-DEHYDROQUINATE DEHYDRATASE FROM AQUIFEX AEOLICUS VF5

Authors :   T. Tanaka, T. S. Kumarevel, A. Ebihara, L. Chen, Z. Q. Fu, J. Chrzas, B. C. S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   04 Apr 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   3-Dehydroquinate Dehydratase, Aquifex Aeolicus Vf5, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. S. Kumarevel, T. Tanaka, S. Kuramitsu, S. Yokoyama
Crystal Structure Of The 3-Dehydroquinate Dehydratase From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
	Chains	:	A, B, C
	EC Number	:	4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A
	Expression System Strain	:	BL21(DE3)CODONPLUS-RIL-X
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5
	Synonym	:	3-DEHYDROQUINASE, TYPE I DHQASE

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2YSW)

(no "Site" information available for 2YSW)

Asymmetric Unit

No.	Residues
1	A:158	-	B:158
2	C:158	-	C:158

(no "Cis Peptide Bond" information available for 2YSW)

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_I	PS01028	Dehydroquinase class I active site.	AROD_AQUAE	88-117	3	A:88-117 B:88-117 C:88-117

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_I	PS01028	Dehydroquinase class I active site.	AROD_AQUAE	88-117	2	A:88-117 B:88-117 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_I	PS01028	Dehydroquinase class I active site.	AROD_AQUAE	88-117	2	- - C:88-117

(no "Exon" information available for 2YSW)

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:219
 aligned with AROD_AQUAE | O66440 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           AROD_AQUAE     1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
               SCOP domains d2yswa_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh...eeeee.hhh...hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh......eeeee.....hhhhhhhhhh..eee............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:88-11------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysw A   1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with AROD_AQUAE | O66440 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           AROD_AQUAE     1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
               SCOP domains d2yswb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh...eeeee.hhh...hhhhhhhhhhhhhhh..eeeee..hhhhh.....hhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh..eee............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:88-11------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysw B   1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with AROD_AQUAE | O66440 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           AROD_AQUAE     1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
               SCOP domains d2yswc_ C: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DHquinase_I-2yswC01 C:3-214                                                                                                                                                                                         ----- Pfam domains (1)
           Pfam domains (2) --DHquinase_I-2yswC02 C:3-214                                                                                                                                                                                         ----- Pfam domains (2)
           Pfam domains (3) --DHquinase_I-2yswC03 C:3-214                                                                                                                                                                                         ----- Pfam domains (3)
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh..eeeee..hhhhh.....hhhhhhhhhh....eeeee..hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhh......eeeee.....hhhhhhhhhh..eee............hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: C:88-11------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ysw C   1 MLIAVPLDDTNFSENLKKAKEKGADIVELRVDQFSDTSLNYVKEKLEEVHSQGLKTILTIRSPEEGGREVKNREELFEELSPLSDYTDIELSSRGLLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIAVKANSYEDVARLLCISRQVEGEKILISMGDYGKISRLAGYVFGSVITYCSLEKAFAPGQIPLEEMVELRKKFYRL 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Aquifex aeolicus [TaxId: 63363] (3)

1a	d2yswa_	A:
1b	d2yswb_	B:
1c	d2yswc_	C:

(no "CATH Domain" information available for 2YSW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DHquinase_I (17)

Aquifex aeolicus (1)

1a	DHquinase_I-2yswC01	C:3-214
1b	DHquinase_I-2yswC02	C:3-214
1c	DHquinase_I-2yswC03	C:3-214

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (AROD_AQUAE | O66440)

molecular function
	GO:0003855	3-dehydroquinate dehydratase activity	Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
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.

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Biological Units
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	AROD_AQUAE \| O66440	:	2egz

2egz	DIFFERENT SPACE GROUP RELATED ID: AAE001000021.2 RELATED DB: TARGETDB

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