1EHY - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF THE EPOXIDE HYDROLASE FROM AGROBACTERIUM RADIOBACTER AD1

Authors :   M. Nardini, I. S. Ridder, H. J. Rozeboom, K. H. Kalk, R. Rink, D. B. Jansse B. W. Dijkstra

Date :   17 Oct 98 (Deposition) - 16 Oct 99 (Release) - 09 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Hydrolase, Alpha/Beta Hydrolase Fold, Epoxide Degradation, Epichlorohydrin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Nardini, I. S. Ridder, H. J. Rozeboom, K. H. Kalk, R. Rink, D. B. Janssen, B. W. Dijkstra
The X-Ray Structure Of Epoxide Hydrolase From Agrobacterium Radiobacter Ad1. An Enzyme To Detoxify Harmful Epoxides.
J. Biol. Chem. V. 274 14579 1999
PubMed-ID: 10329649 | Reference-DOI: 10.1074/JBC.274.21.14579
(for further references see the PDB file header)

Molecule 1 - PROTEIN (SOLUBLE EPOXIDE HYDROLASE)
	Chains	:	A, B, C, D
	EC Number	:	3.3.2.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGELAF+
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS
	Organism Taxid	:	358
	Strain	:	AD1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:181 , SER A:184 , TYR A:185 , ARG A:186 , HOH A:352 , HOH A:411	BINDING SITE FOR RESIDUE K A 295
2	AC2	SOFTWARE	ASP B:181 , SER B:184 , ARG B:186 , HOH B:359 , HOH B:440	BINDING SITE FOR RESIDUE K B 296
3	AC3	SOFTWARE	ASP C:181 , SER C:184 , TYR C:185 , ARG C:186 , HOH C:559	BINDING SITE FOR RESIDUE K C 297
4	AC4	SOFTWARE	ASP D:181 , SER D:184 , TYR D:185 , ARG D:186	BINDING SITE FOR RESIDUE K D 298

Asymmetric Unit

No.	Residues
1	C:248	-	D:248

Asymmetric Unit

No.	Residues
1	Trp A:38	-	Pro A:39
2	Trp B:38	-	Pro B:39
3	Trp C:38	-	Pro C:39
4	Trp D:38	-	Pro D:39

(no "SAP(SNP)/Variant" information available for 1EHY)

(no "PROSITE Motif" information available for 1EHY)

(no "Exon" information available for 1EHY)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:282
 aligned with O31243_RHIRD | O31243 from UniProtKB/TrEMBL  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         O31243_RHIRD     2 TIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDFGPVYFGLGHVHESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
               SCOP domains d1ehya_ A: Bacterial epoxide hydrolase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ehyA00 A:2-294  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh..eeeee....eeeeeeee..eeeeee......hhhhhhhhhhhhh.eeeeee...............hhhh.hhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhh.hhh...eeee.......-----------..hhhhhhh.hhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh..........hhh......eeeeee........hhhhhhhhhh...eeeeee......hhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ehy A   2 AIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDF-----------ESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                                                                                                                                                 137         149

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with O31243_RHIRD | O31243 from UniProtKB/TrEMBL  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         O31243_RHIRD     2 TIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDFGPVYFGLGHVHESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
               SCOP domains d1ehyb_ B: Bacterial epoxide hydrolase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ehyB00 B:2-294  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh..eeeee....eeeeeeee..eeeeee......hhhhhhhhhhhhh.eeeeee...............hhhh.hhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhh.hhh...eeee.......-----------..hhhhhhh.hhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh..........hhh......eeeeee........hhhhhhhhh....eeeeee......hhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ehy B   2 AIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDF-----------ESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                                                                                                                                                 137         149

Chain C from PDB  Type:PROTEIN  Length:282
 aligned with O31243_RHIRD | O31243 from UniProtKB/TrEMBL  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         O31243_RHIRD     2 TIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDFGPVYFGLGHVHESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
               SCOP domains d1ehyc_ C: Bacterial epoxide hydrolase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ehyC00 C:2-294  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh..eeeee....eeeeeeee..eeeeee......hhhhhhhhhhhhh.eeeeee...............hhhh.hhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhh.hhh...eeee.......-----------..hhhhhhh.hhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh..........hhh......eeeeee.....hhhhhhhhhhhh....eeeeee......hhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ehy C   2 AIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDF-----------ESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                                                                                                                                                 137         149

Chain D from PDB  Type:PROTEIN  Length:282
 aligned with O31243_RHIRD | O31243 from UniProtKB/TrEMBL  Length:294

    Alignment length:293
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         O31243_RHIRD     2 TIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDFGPVYFGLGHVHESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
               SCOP domains d1ehyd_ D: Bacterial epoxide hydrolase                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ehyD00 D:2-294  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh..eeeee....eeeeeeee..eeeeee......hhhhhhhhhhhhh.eeeeee...............hhhh.hhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhh.hhh...eeee.......-----------..hhhhhhh.hhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhh..........hhh......eeeeee.....hhhhhhhhhhhhh...eeeeee......hhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ehy D   2 AIRRPEDFKHYEVQLPDVKIHYVREGAGPTLLLLHGWPGFWWEWSKVIGPLAEHYDVIVPDLRGFGDSEKPDLNDLSKYSLDKAADDQAALLDALGIEKAYVVGHDFAAIVLHKFIRKYSDRVIKAAIFDPIQPDF-----------ESWYSQFHQLDMAVEVVGSSREVCKKYFKHFFDHWSYRDELLTEEELEVHVDNCMKPDNIHGGFNYYRANIRPDAALWTDLDHTMSDLPVTMIWGLGDTCVPYAPLIEFVPKYYSNYTMETIEDCGHFLMVEKPEIAIDRIKTAFR 294
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     |   -       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
                                                                                                                                                                 137         149

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Epoxide hydrolase (20)

Protein domain: Bacterial epoxide hydrolase (4)

Agrobacterium radiobacter [TaxId: 358] (1)

1a	d1ehya_	A:
1b	d1ehyb_	B:
1c	d1ehyc_	C:
1d	d1ehyd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Agrobacterium tumefaciens. Organism_taxid: 358. Strain: ad1. (1)

1a	1ehyA00	A:2-294
1b	1ehyB00	B:2-294
1c	1ehyC00	C:2-294
1d	1ehyD00	D:2-294

(no "Pfam Domain" information available for 1EHY)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O31243_RHIRD | O31243)

molecular function
	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:0016787		hydrolase activity		Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.

Asymmetric Unit
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	1ehy
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