3TH1 - JenaLib

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Title :   CRYSTAL STRUCTURE OF CHLOROCATECHOL 1,2-DIOXYGENASE FROM PSEUDOMONAS PUTIDA

Authors :   J. K. Rustiguel, M. C. Nonato

Date :   18 Aug 11 (Deposition) - 22 Aug 12 (Release) - 22 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

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

Keywords :   Catechol 1, 2-Dioxygenase Family, Oxidoreductase, Iron Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. K. Rustiguel, L. R. S. Barbosa, A. P. U. Araujo, M. C. Nonato
Crystal Structure Of Chlorocatechol 1, 2-Dioxygenase From Pseudomonas Putida
To Be Published
PubMed: search

Molecule 1 - CHLOROCATECHOL 1,2-DIOXYGENASE
	Chains	:	A, B, C
	EC Number	:	1.13.11.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	CLCA
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 12)

No.	Name	Count	Type	Full Name
1	3PH	2	Ligand/Ion	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
2	ACT	1	Ligand/Ion	ACETATE ION
3	DTD	2	Ligand/Ion	DITHIANE DIOL
4	FE	3	Ligand/Ion	FE (III) ION
5	GOL	2	Ligand/Ion	GLYCEROL
6	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	3PH	2	Ligand/Ion	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
2	ACT	2	Ligand/Ion	ACETATE ION
3	DTD	2	Ligand/Ion	DITHIANE DIOL
4	FE	-1	Ligand/Ion	FE (III) ION
5	GOL	-1	Ligand/Ion	GLYCEROL
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	3PH	1	Ligand/Ion	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
2	ACT	-1	Ligand/Ion	ACETATE ION
3	DTD	1	Ligand/Ion	DITHIANE DIOL
4	FE	-1	Ligand/Ion	FE (III) ION
5	GOL	2	Ligand/Ion	GLYCEROL
6	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR C:130 , TYR C:164 , HIS C:188 , HIS C:190	BINDING SITE FOR RESIDUE FE C 300
02	AC2	SOFTWARE	TYR B:130 , TYR B:164 , HIS B:188 , HIS B:190	BINDING SITE FOR RESIDUE FE B 300
03	AC3	SOFTWARE	ILE B:73 , PRO B:76 , TYR B:164 , ARG B:185	BINDING SITE FOR RESIDUE DTD B 301
04	AC4	SOFTWARE	GLU B:29 , ALA B:32 , GLY B:33 , TYR B:36 , LEU B:37 , LEU B:50 , ARG B:174 , HIS B:178 , VAL C:5 , VAL C:8	BINDING SITE FOR RESIDUE 3PH B 302
05	AC5	SOFTWARE	ASP B:51 , TYR C:30 , VAL C:34 , ASP C:35	BINDING SITE FOR RESIDUE GOL B 303
06	AC6	SOFTWARE	LYS A:211 , TRP A:212 , ASP A:215 , TRP B:212 , ASP B:214 , ASP B:215	BINDING SITE FOR RESIDUE GOL B 306
07	AC7	SOFTWARE	TYR A:130 , TYR A:164 , HIS A:188 , HIS A:190 , DTD A:301	BINDING SITE FOR RESIDUE FE A 300
08	AC8	SOFTWARE	ASP A:51 , ILE A:73 , GLY A:75 , PRO A:76 , TYR A:164 , ARG A:185 , FE A:300	BINDING SITE FOR RESIDUE DTD A 301
09	AC9	SOFTWARE	VAL A:5 , VAL A:8 , ALA A:32 , GLY A:33 , TYR A:36 , LEU A:37 , LEU A:50 , LEU A:54 , ARG A:174 , HIS A:178	BINDING SITE FOR RESIDUE 3PH A 302
10	BC1	SOFTWARE	ARG A:103 , ASN A:153	BINDING SITE FOR RESIDUE MG A 303
11	BC2	SOFTWARE	THR A:239 , ASP A:241	BINDING SITE FOR RESIDUE MG A 304
12	BC3	SOFTWARE	SER A:56 , THR A:57 , GLU A:60 , HIS A:219	BINDING SITE FOR RESIDUE ACT A 305

(no "SS Bond" information available for 3TH1)

Asymmetric Unit

No.	Residues
1	Glu A:86	-	Gly A:87
2	Gly C:152	-	Asn C:153
3	Glu C:245	-	Arg C:246

(no "SAP(SNP)/Variant" information available for 3TH1)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTRADIOL_DIOXYGENAS	PS00083	Intradiol ring-cleavage dioxygenases signature.	CLCA_PSEPU	102-130	3	A:102-130 B:102-130 C:102-130

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTRADIOL_DIOXYGENAS	PS00083	Intradiol ring-cleavage dioxygenases signature.	CLCA_PSEPU	102-130	2	A:102-130 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	INTRADIOL_DIOXYGENAS	PS00083	Intradiol ring-cleavage dioxygenases signature.	CLCA_PSEPU	102-130	2	- B:102-130 C:102-130

(no "Exon" information available for 3TH1)

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:246
 aligned with CLCA_PSEPU | P11451 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           CLCA_PSEPU     1 MDKRVAEVAGAIVEAVRKILLDKRVTEAEYRAGVDYLTEVAQTRETALLLDVFLNSTIIEGKAQRSRTSAPAIQGPYFLEGAPVVEGVLKTYDTDDHKPLIIRGTVRSDTGELLAGAVIDVWHSTPDGLYSGIHDNIPVDYYRGKLVTDSQGNYRVRTTMPVPYQIPYEGPTGRLLGHLGSHTWRPAHVHFKVRKDGFEPLTTQYYFEGGKWVDDDCCHGVTPDLITPETIEDGVRVMTLDFVIER 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...................................eeeeeeeeee.........eeeee....................eeeee.....eeeeeee....ee....hhhhhhhhhh....ee..eeeeeee......eeeeeee..............hhh.ee........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3th1 A   1 MDKRVAEVAGAIVEAVRKILLDKRVTEAEYRAGVDYLTEVAQTRETALLLDVFLNSTIIEGKAQRSRTSAPAIQGPYFLEGAPVVEGVLKTYDTDDHKPLIIRGTVRSDTGELLAGAVIDVWHSTPDGLYSGIHDNIPVDYYRGKLVTDSQGNYRVRTTMPVPYQIPYEGPTGRLLGHLGSHTWRPAHVHFKVRKDGFEPLTTQYYFEGGKWVDDDCCHGVTPDLITPETIEDGVRVMTLDFVIER 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with CLCA_PSEPU | P11451 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           CLCA_PSEPU     1 MDKRVAEVAGAIVEAVRKILLDKRVTEAEYRAGVDYLTEVAQTRETALLLDVFLNSTIIEGKAQRSRTSAPAIQGPYFLEGAPVVEGVLKTYDTDDHKPLIIRGTVRSDTGELLAGAVIDVWHSTPDGLYSGIHDNIPVDYYRGKLVTDSQGNYRVRTTMPVPYQIPYEGPTGRLLGHLGSHTWRPAHVHFKVRKDGFEPLTTQYYFEGGKWVDDDCCHGVTPDLITPETIEDGVRVMTLDFVIER 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh................................eeeeee.....-.......eeeee....................eeeee......eeeeee....ee....hhhhhhhhhh....ee..eeeee.--......eeeeee..............hhh.ee..ee....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3th1 B   1 MDKRVAEVAGAIVEAVRKILLDKRVTEAEYRAGVDYLTEVAQTRETALLLDVFLNSTIIEGKAQRSRTSAPAIQGPYFLEGAPVVEGVLKTYDTDDHKPLIIRGTVRSD-GELLAGAVIDVWHSTPDGLYSGIHDNIPVDYYRGKLVTDSQGNYRVRTTMPVPYQIPYEGPTGRLLGHLGSHTWRPAHVHFKV--DGFEPLTTQYYFEGGKWVDDDCCHGVTPDLITPETIEDGVRVMTLDFVIER 246
                                    10        20        30        40        50        60        70        80        90       100        |-|      120       130       140       150       160       170       180       190  |  | 200       210       220       230       240      
                                                                                                                                      109 |                                                                               193  |                                                  
                                                                                                                                        111                                                                                  196

Chain C from PDB  Type:PROTEIN  Length:238
 aligned with CLCA_PSEPU | P11451 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           CLCA_PSEPU     1 MDKRVAEVAGAIVEAVRKILLDKRVTEAEYRAGVDYLTEVAQTRETALLLDVFLNSTIIEGKAQRSRTSAPAIQGPYFLEGAPVVEGVLKTYDTDDHKPLIIRGTVRSDTGELLAGAVIDVWHSTPDGLYSGIHDNIPVDYYRGKLVTDSQGNYRVRTTMPVPYQIPYEGPTGRLLGHLGSHTWRPAHVHFKVRKDGFEPLTTQYYFEGGKWVDDDCCHGVTPDLITPETIEDGVRVMTLDFVIER 246
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh............-.....---............eeeeeeeee.........eeeee............--......eeeee.....eeeeee.....ee....hhhhhhhhhh....ee..eeeeeeee..eeeeeeeeee..............hhh.ee......--.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------INTRADIOL_DIOXYGENAS         -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3th1 C   1 MDKRVAEVAGAIVEAVRKILLDKRVTEAEYRAGVDYLTEVAQTRETALLLDVFLNSTIIEGKAQRSRTSAPAIQGPYF-EGAPV---VLKTYDTDDHKPLIIRGTVRSDTGELLAGAVIDVWHSTPDGLYSGIH--IPVDYYRGKLVTDSQGNYRVRTTMPVPYQIPYEGPTGRLLGHLGSHTWRPAHVHFKVRKDGFEPLTTQYYFEGGKWVDDDCCHGVTPDLITPETIED--RVMTLDFVIER 246
                                    10        20        30        40        50        60        70       |80   |   |90       100       110       120       130   |  |140       150       160       170       180       190       200       210       220       230  |  | 240      
                                                                                                        78 |  84  88                                           134  |                                                                                             233  |          
                                                                                                          80                                                      137                                                                                                236

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	-	→ 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 '\|'

(no "SCOP Domain" information available for 3TH1)

(no "CATH Domain" information available for 3TH1)

(no "Pfam Domain" information available for 3TH1)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CLCA_PSEPU | P11451)

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:0018576	catechol 1,2-dioxygenase activity	Catalysis of the reaction: catechol + O2 = cis,cis-muconate.
	GO:0018575	chlorocatechol 1,2-dioxygenase activity	Catalysis of the reaction: 3,6-dichlorocatechol + O2 = 2 H+ + 2,5-dichloro-cis,cis-muconate.
	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:0008199	ferric iron binding	Interacting selectively and non-covalently with ferric iron, Fe(III).
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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.
	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
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:0009712	catechol-containing compound metabolic process	The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent.
	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.

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	Cis Peptide Bonds
		Glu A:86 - Gly A:87	[ RasMol ]
		Glu C:245 - Arg C:246	[ RasMol ]
		Gly C:152 - Asn C:153	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (6, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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