3JS3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE (AROD) FROM CLOSTRIDIUM DIFFICILE WITH COVALENT REACTION INTERMEDIATE

Authors :   G. Minasov, S. H. Light, L. Shuvalova, I. Dubrovska, J. Winsor, S. N. Pet W. F. Anderson, Center For Structural Genomics Of Infectious (Csgid)

Date :   09 Sep 09 (Deposition) - 22 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Type I 3-Dehydroquinate Dehydratase, Arod, Covalent Reaction Intermediate, Amino-Acid Biosynthesis, Aromatic Amino Acid Biosynthesis, Lyase, Schiff Base, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. H. Light, G. Minasov, L. Shuvalova, M. E. Duban, M. Caffrey, W. F. Anderson, A. Lavie
Insights Into The Mechanism Of Type I Dehydroquinate Dehydratases From Structures Of Reaction Intermediates.
J. Biol. Chem. V. 286 3531 2011
PubMed-ID: 21087925 | Reference-DOI: 10.1074/JBC.M110.192831

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AROD, CD2217
	Organism Scientific	:	CLOSTRIDIUM DIFFICILE
	Organism Taxid	:	272563
	Strain	:	630
	Synonym	:	3-DEHYDROQUINASE, TYPE I DHQASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	DHS	4	Ligand/Ion	3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	DHS	2	Ligand/Ion	3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	DHS	2	Ligand/Ion	3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:47 , ARG A:49 , ARG A:83 , LYS A:171 , MET A:204 , ARG A:214 , PHE A:226 , SER A:233 , ALA A:234 , GLN A:237 , HOH A:282 , HOH A:304	BINDING SITE FOR RESIDUE DHS A 301
2	AC2	SOFTWARE	GLU B:47 , ARG B:49 , ARG B:83 , HIS B:144 , LYS B:171 , MET B:204 , ARG B:214 , PHE B:226 , SER B:233 , ALA B:234 , GLN B:237 , HOH B:321 , HOH B:322	BINDING SITE FOR RESIDUE DHS B 301
3	AC3	SOFTWARE	GLU C:47 , ARG C:49 , ARG C:83 , LYS C:171 , MET C:204 , ARG C:214 , PHE C:226 , SER C:233 , ALA C:234 , GLN C:237 , HOH C:278	BINDING SITE FOR RESIDUE DHS C 301
4	AC4	SOFTWARE	GLU D:47 , ARG D:49 , ARG D:83 , HIS D:144 , LYS D:171 , MET D:204 , ARG D:214 , PHE D:226 , SER D:233 , ALA D:234 , GLN D:237 , HOH D:320	BINDING SITE FOR RESIDUE DHS D 301

Asymmetric Unit

No.	Residues
1	A:42	-	D:42
2	B:42	-	C:42

(no "Cis Peptide Bond" information available for 3JS3)

(no "SAP(SNP)/Variant" information available for 3JS3)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEHYDROQUINASE_I	PS01028	Dehydroquinase class I active site.	AROD_PEPD6	115-145	4	A:115-145 B:115-145 C:115-145 D:115-145

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_PEPD6	115-145	2	A:115-145 B:115-145 - -

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_PEPD6	115-145	2	- - C:115-145 D:115-145

(no "Exon" information available for 3JS3)

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:253
 aligned with AROD_PEPD6 | Q186A6 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:253
                                    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   
           AROD_PEPD6     1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
               SCOP domains d3js3a_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3js3A00 A:1-253 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: A:115-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js3 A   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
                                    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

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with AROD_PEPD6 | Q186A6 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:253
                                    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   
           AROD_PEPD6     1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
               SCOP domains d3js3b_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3js3B00 B:1-253 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: B:115-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js3 B   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
                                    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

Chain C from PDB  Type:PROTEIN  Length:253
 aligned with AROD_PEPD6 | Q186A6 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:253
                                    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   
           AROD_PEPD6     1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
               SCOP domains d3js3c_ C: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3js3C00 C:1-253 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhh......eeeee.hhh....hhhhhhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: C:115-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js3 C   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
                                    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

Chain D from PDB  Type:PROTEIN  Length:253
 aligned with AROD_PEPD6 | Q186A6 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:253
                                    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   
           AROD_PEPD6     1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
               SCOP domains d3js3d_ D: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3js3D00 D:1-253 Aldolase class I                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee.....eeeeee...hhhhhhhhhhhhh.....eeeee.hhh....hhhhhhhhhhhhhhhh....eeee..hhhhh.....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh...eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhh..eee............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------DEHYDROQUINASE_I  PDB: D:115-14------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3js3 D   1 MKRKVQVKNITIGEGRPKICVPIIGKNKKDIIKEAKELKDACLDIIEWRVDFFENVENIKEVKEVLYELRSYIHDIPLLFTFRSVVEGGEKLISRDYYTTLNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKKEEIVSRLCRMQELGADLPKIAVMPQNEKDVLVLLEATNEMFKIYADRPIITMSMSGMGVISRLCGEIFGSALTFGAAKSVSAPGQISFKELNSVLNLLHKS 253
                                    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

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)

Clostridium difficile [TaxId: 272563] (2)

1a	d3js3a_	A:
1b	d3js3b_	B:
1c	d3js3c_	C:
1d	d3js3d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Clostridium difficile 630. Organism_taxid: 272563. Strain: 630. (1)

1a	3js3A00	A:1-253
1b	3js3B00	B:1-253
1c	3js3C00	C:1-253
1d	3js3D00	D:1-253

(no "Pfam Domain" information available for 3JS3)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (AROD_PEPD6 | Q186A6)

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:0046279	3,4-dihydroxybenzoate biosynthetic process	The chemical reactions and pathways resulting in the formation of 3,4-dihydroxybenzoate.
	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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(no "Related Entries Specified in the PDB File" available for 3JS3)

Description

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SS Bonds (2, 2)

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