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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE 2,3-DIOXYGENASE LAPB FROM PSEUDOMONAS IN THE COMPLEX WITH 4-METHYLCATECHOL

Authors :   J. -H. Cho, S. Rhee

Date :   05 Jun 09 (Deposition) - 20 Oct 09 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Repeated Motifs, Aromatic Hydrocarbons Catabolism, Dioxygenase, Iron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. -H. Cho, D. -K. Jung, K. Lee, S. Rhee
Crystal Structure And Functional Analysis Of The Extradiol Dioxygenase Lapb From A Long-Chain Alkylphenol Degradation Pathway In Pseudomonas
J. Biol. Chem. V. 284 34321 2009
PubMed-ID: 19828456 | Reference-DOI: 10.1074/JBC.M109.031054

Molecule 1 - CATECHOL 2,3-DIOXYGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.13.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PSEUDOMONAS SP. KL28
	Organism Taxid	:	237609
	Strain	:	KCTC 22206

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	FE	4	Ligand/Ion	FE (III) ION
2	MCT	3	Ligand/Ion	4-METHYLCATECHOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:154 , HIS A:216 , GLU A:267 , MCT A:311	BINDING SITE FOR RESIDUE FE A 310
2	AC2	SOFTWARE	HIS A:154 , TRP A:193 , HIS A:201 , HIS A:216 , HIS A:248 , VAL A:250 , THR A:251 , TYR A:257 , GLU A:267 , FE A:310	BINDING SITE FOR RESIDUE MCT A 311
3	AC3	SOFTWARE	HIS B:154 , HIS B:216 , GLU B:267 , MCT B:311	BINDING SITE FOR RESIDUE FE B 310
4	AC4	SOFTWARE	HIS B:154 , TRP B:193 , HIS B:201 , HIS B:216 , HIS B:248 , VAL B:250 , THR B:251 , TYR B:257 , GLU B:267 , FE B:310	BINDING SITE FOR RESIDUE MCT B 311
5	AC5	SOFTWARE	HIS C:154 , HIS C:216 , GLU C:267 , MCT C:311	BINDING SITE FOR RESIDUE FE C 310
6	AC6	SOFTWARE	HIS C:154 , TRP C:193 , HIS C:201 , HIS C:216 , HIS C:248 , VAL C:250 , THR C:251 , TYR C:257 , GLU C:267 , FE C:310	BINDING SITE FOR RESIDUE MCT C 311
7	AC7	SOFTWARE	HIS D:154 , HIS D:216 , SER D:218 , GLU D:267	BINDING SITE FOR RESIDUE FE D 310

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

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

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

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

(no "Exon" information available for 3HPY)

Asymmetric/Biological 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:288
 aligned with Q7WYF5_9PSED | Q7WYF5 from UniProtKB/TrEMBL  Length:309

    Alignment length:288
                                    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        
         Q7WYF5_9PSED     2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNF 289
               SCOP domains d3hpya1 A:2-146 automated matches                                                                                                                d3hpya2 A:147-289 automated matches                                                                                                             SCOP domains
               CATH domains 3hpyA01 A:2-150 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                      3hpyA02 A:151-289 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee.hhhhhhhhhhhh...eeeee.....eeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhhh...eee..........eeeee.....eeeee..................hhhhhh.....eeeeeeeee.hhhhhhhhhhhh...eeeeeee......eeeeeee.......eeeee.....eeeeeeee..hhhhhhhhhhhhhhh........ee.....eeeeeee.....eeeeeee..........eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hpy A   2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNF 289
                                    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

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with Q7WYF5_9PSED | Q7WYF5 from UniProtKB/TrEMBL  Length:309

    Alignment length:288
                                    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        
         Q7WYF5_9PSED     2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNF 289
               SCOP domains d3hpyb1 B:2-146 automated matches                                                                                                                d3hpyb2 B:147-289 automated matches                                                                                                             SCOP domains
               CATH domains 3hpyB01 B:2-150 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                      3hpyB02 B:151-289 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee.hhhhhhhhhhhh...eeeee.....eeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhhh...eee..........eeeee.....eeeee..................hhhhhh.....eeeeeeeee.hhhhhhhhhhhh...eeeeeee......eeeeeee.......eeeee.....eeeeeeee..hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee...........eeehhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3hpy B   2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNF 289
                                    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

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with Q7WYF5_9PSED | Q7WYF5 from UniProtKB/TrEMBL  Length:309

    Alignment length:296
                                    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      
         Q7WYF5_9PSED     2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNFAQGLDYPQ 297
               SCOP domains d3hpyc1 C:2-146 automated matches                                                                                                                d3hpyc2 C:147-297 automated matches                                                                                                                     SCOP domains
               CATH domains 3hpyC01 C:2-150 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                      3hpyC02 C:151-297 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee.hhhhhhhhhhhh...eeeee.....eeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhhh..eeee..........eeeee.....eeeee..................hhhhhh.....eeeeeeeee.hhhhhhhhhhhh...eeeeeee......eeeeeee.......eeeee.....eeeeeeee..hhhhhhhhhhhhhhh...eeeeeee.hhhh.eeeeee.....eeeeee...........eee...hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpy C   2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNFAQGLDYPQ 297
                                    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

Chain D from PDB  Type:PROTEIN  Length:296
 aligned with Q7WYF5_9PSED | Q7WYF5 from UniProtKB/TrEMBL  Length:309

    Alignment length:296
                                    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      
         Q7WYF5_9PSED     2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNFAQGLDYPQ 297
               SCOP domains d3hpyd1 D:2-146 automated matches                                                                                                                d3hpyd2 D:147-297 automated matches                                                                                                                     SCOP domains
               CATH domains 3hpyD01 D:2-150 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                      3hpyD02 D:151-297 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee.hhhhhhhhhhhh...eeeee....eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhhh...eee..........eeeee.....eeeee..................hhhhhh.....eeeeeeeee.hhhhhhhhhhhh...eeeeeee......eeeeeee.......eeeee.....eeeeeeee..hhhhhhhhhhhhhhh...eeeeeee.hhhh.eeeeee.....eeeee............eeehhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hpy D   2 AMTGVLRPGHAQVRVLNLEEGIHFYRNVLGLVETGRDDQGRVYFKCWDERDHSCYIIREADTAGIDFFGFKVLDKATLEKLDADLQAYGLTTTRIPAGEMLETGERVRFELPSGHLIELYAEKTCVGNGISEVNPAPWNAQREHGIAPIQLDHCLLYGPNIAEVQKIFTEVLGFYLVERVLSPDGDSDMGIWLSCSHKVHDIAFVEYPEKGKLHHCSFLLESWEQVLRAGDIMSMNEVNVDIGPTRHGVTRGCTIYAWDPSGNRFETFMGGYHPYPDYEPLSWTYDNFAQGLDYPQ 297
                                    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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Superfamily: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase (136)

Family: automated matches (34)

Protein domain: automated matches (34)

Pseudomonas sp. [TaxId: 237609] (3)

1a	d3hpya1	A:2-146
1b	d3hpyb1	B:2-146
1c	d3hpyb2	B:147-289
1d	d3hpyc1	C:2-146
1e	d3hpyc2	C:147-297
1f	d3hpyd1	D:2-146
1g	d3hpyd2	D:147-297
1h	d3hpya2	A:147-289

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 (113)

Homologous Superfamily: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 (106)

Kl28 (Pseudomonas sp) (3)

1a	3hpyA02	A:151-289
1b	3hpyB02	B:151-289
1c	3hpyA01	A:2-150
1d	3hpyB01	B:2-150
1e	3hpyC01	C:2-150
1f	3hpyD01	D:2-150
1g	3hpyC02	C:151-297
1h	3hpyD02	D:151-297

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q7WYF5_9PSED | Q7WYF5)

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:0018577	catechol 2,3-dioxygenase activity	Catalysis of the reaction: catechol + O2 = 2-hydroxymuconate semialdehyde.
	GO:0051213	dioxygenase activity	Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
	GO:0008198	ferrous iron binding	Interacting selectively and non-covalently with ferrous iron, Fe(II).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0006725	cellular aromatic compound metabolic process	The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3hpy)

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	3hpy
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 8)

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