3GZX - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE IN COMPLEX WITH BIPHENYL FROM COMAMONAS TESTOSTERONI SP. STRAIN B-356

Authors :   P. Kumar, C. L. Colbert, J. T. Bolin

Date :   08 Apr 09 (Deposition) - 05 May 10 (Release) - 06 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.58

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Dioxygenase, Rieskie, Non-Heme Iron, Aromatic Hydrocarbons Catabolism, Iron, Iron-Sulfur, Metal-Binding, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Colbert, N. Y. Agar, P. Kumar, M. N. Chakko, S. C. Sinha, J. B. Powlowski, L. D. Eltis, J. T. Bolin
Structural Characterization Of Pandoraea Pnomenusa B-356 Biphenyl Dioxygenase Reveals Features Of Potent Polychlorinated Biphenyl-Degrading Enzymes
Plos One V. 8 52550 2013
PubMed-ID: 23308114 | Reference-DOI: 10.1371/JOURNAL.PONE.0052550

Molecule 1 - BIPHENYL DIOXYGENASE SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	1.14.12.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BPHA
	Organism Common	:	PSEUDOMONAS TESTOSTERONI
	Organism Scientific	:	COMAMONAS TESTOSTERONI
	Organism Taxid	:	285
	Synonym	:	BIPHENYL 2,3-DIOXYGENASE

Molecule 2 - BIPHENYL DIOXYGENASE SUBUNIT BETA
	Chains	:	B
	EC Number	:	1.14.12.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	BPHE
	Organism Common	:	PSEUDOMONAS TESTOSTERONI
	Organism Scientific	:	COMAMONAS TESTOSTERONI
	Organism Taxid	:	285
	Synonym	:	BIPHENYL 2,3-DIOXYGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 6)

No.	Name	Count	Type	Full Name
1	BNL	1	Ligand/Ion	BIPHENYL
2	FE2	1	Ligand/Ion	FE (II) ION
3	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
4	GOL	2	Ligand/Ion	GLYCEROL
5	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Biological Unit 1 (5, 18)

No.	Name	Count	Type	Full Name
1	BNL	3	Ligand/Ion	BIPHENYL
2	FE2	3	Ligand/Ion	FE (II) ION
3	FES	3	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
4	GOL	6	Ligand/Ion	GLYCEROL
5	MES	3	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:226 , HIS A:233 , HIS A:239 , ASP A:386 , HOH A:458	BINDING SITE FOR RESIDUE FE2 A 701
2	AC2	SOFTWARE	CYS A:100 , HIS A:102 , ARG A:103 , CYS A:120 , HIS A:123 , TRP A:125	BINDING SITE FOR RESIDUE FES A 700
3	AC3	SOFTWARE	GLN A:226 , PHE A:227 , ASP A:230 , HIS A:233 , GLY A:319 , HIS A:321 , LEU A:331	BINDING SITE FOR RESIDUE BNL A 702
4	AC4	SOFTWARE	LEU A:74 , ASP A:111 , GLY A:112 , HOH A:661 , GOL A:706 , HOH A:737 , HOH A:756 , ARG B:62	BINDING SITE FOR RESIDUE GOL A 705
5	AC5	SOFTWARE	HIS A:66 , PRO A:68 , LYS A:69 , ASP A:72 , GOL A:705 , HOH A:818	BINDING SITE FOR RESIDUE GOL A 706
6	AC6	SOFTWARE	ASN A:279 , HOH A:819 , ARG B:118 , MET B:120 , ASP B:121 , HOH B:515 , HOH B:617	BINDING SITE FOR RESIDUE MES B 704

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

Asymmetric Unit

No.	Residues
1	Phe A:325	-	Pro A:326
2	Asp B:103	-	Pro B:104

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIESKE	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.	BPHA_COMTE	58-174	1	A:58-174
2	RING_HYDROXYL_ALPHA	PS00570	Bacterial ring hydroxylating dioxygenases alpha-subunit signature.	BPHA_COMTE	100-123	1	A:100-123

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIESKE	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.	BPHA_COMTE	58-174	3	A:58-174
2	RING_HYDROXYL_ALPHA	PS00570	Bacterial ring hydroxylating dioxygenases alpha-subunit signature.	BPHA_COMTE	100-123	3	A:100-123

(no "Exon" information available for 3GZX)

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:440
 aligned with BPHA_COMTE | Q46372 from UniProtKB/Swiss-Prot  Length:457

    Alignment length:440
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457
           BPHA_COMTE    18 NWTPDAIRALVDQDNGKLDARIYADQDLYQLELERVFGRSWLMLGHETHIPKIGDYLTTYMGEDPVIMVRQKDQSIKVFLNQCRHRGMRIVRSDGGNAKAFTCTYHGWAYDIAGNLVNVPFEKEAFCDKKEGDCGFDKADWGPLQARVETYKGLVFANWDPEAPDLKTYLSDAMPYMDVMLDRTEAGTEAIGGIQKWVIPCNWKFAAEQFCSDMYHAGTMSHLSGVLAGLPPEMDLTQIQLSKNGNQFRSAWGGHGAGWFINDSSILLSVVGPKITQYWTQGPAAEKAARRVPQLPILDMFGQHMTVFPTCSFLPGINTIRTWHPRGPNEVEVWAFVLVDADAPEDIKEEFRLQNIRTFNAGGVFEQDDGENWVEIQRVMRGHKAKSTSLCAKMGLNVPNKNNPAYPGKTAYVYAEEAARGMYHHWSRMMSEPSWDTLKP 457
               SCOP domains d3gzxa1 A:18-178 automated matches                                                                                                                               d3gzxa2 A:179-457 automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3gzxA01 A:18-56,A:188-457              3gzxA02 A:57-187 'Rieske'-like iron-sulphur domains                                                                                3gzxA01 A:18-56,A:188-457 Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.ee....eee.hhhhhhhhhhhhhhhh.....eeeee.hhh....eeeeeee..eeeeeee.....eeeee..............eee..eee......eee....eee..hhhhhh..........hhhhh...eeeeeee..eeeee......hhhhhh..hhhhhhhhhh.....eee....eeeee..hhhhhhhhhhhh........hhhhhhhh...............eeeee......eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee...eee.....eeeeeee.....eeeeeeeeee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhh.eee.................eeee...hhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------RIESKE  PDB: A:58-174 UniProt: 58-174                                                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------RING_HYDROXYL_ALPHA     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gzx A  18 NWTPDAIRALVDQDNGKLDARIYADQDLYQLELERVFGRSWLMLGHETHIPKIGDYLTTYMGEDPVIMVRQKDQSIKVFLNQCRHRGMRIVRSDGGNAKAFTCTYHGWAYDIAGNLVNVPFEKEAFCDKKEGDCGFDKADWGPLQARVETYKGLVFANWDPEAPDLKTYLSDAMPYMDVMLDRTEAGTEAIGGIQKWVIPCNWKFAAEQFCSDMYHAGTMSHLSGVLAGLPPEMDLTQIQLSKNGNQFRSAWGGHGAGWFINDSSILLSVVGPKITQYWTQGPAAEKAARRVPQLPILDMFGQHMTVFPTCSFLPGINTIRTWHPRGPNEVEVWAFVLVDADAPEDIKEEFRLQNIRTFNAGGVFEQDDGENWVEIQRVMRGHKAKSTSLCAKMGLNVPNKNNPAYPGKTAYVYAEEAARGMYHHWSRMMSEPSWDTLKP 457
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with BPHE_COMTE | Q46373 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
           BPHE_COMTE     1 MISTPLSKEFEWPAKPVSLELQHQVEQFYYREAQLLDHHAFQAWFALLAEDIHYWMPIRTVRTAREQGLEYVPAGANAHFDDTHATMYGRIRQKTSDLNWAEDPPSRTRHLVSNVIVREMDTPGTLEVASAFLLYRSRLERQVDVFAGERRDVLRIADNPLGFQIAKRTIILDQSTVLANNLSVFF 186
               SCOP domains d3gzxb_ B: automated matches                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeeeee.....hhhhhhhh.......eeeeehhhhhhhhhhhhh...hhhhh...eeeeeeeeeeeee.....eeeeeeeeeeeeee...eeeeeeeeeeeeeee......eeeeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gzx B   1 MISTPLSKEFEWPAKPVSLELQHQVEQFYYREAQLLDHHAFQAWFALLAEDIHYWMPIRTVRTAREQGLEYVPAGANAHFDDTHATMYGRIRQKTSDLNWAEDPPSRTRHLVSNVIVREMDTPGTLEVASAFLLYRSRLERQVDVFAGERRDVLRIADNPLGFQIAKRTIILDQSTVLANNLSVFF 186
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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 '\|'

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

Asymmetric Unit(hide GO term definitions)

Chain A (BPHA_COMTE | Q46372)

molecular function
	GO:0051537	2 iron, 2 sulfur cluster binding	Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0018687	biphenyl 2,3-dioxygenase activity	Catalysis of the reaction: biphenyl + NADH + H+ + O2 = (2R,3S)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+. This reaction requires Fe2+.
	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:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	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:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0016708	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and two atoms of oxygen are incorporated into one 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: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.

Chain B (BPHE_COMTE | Q46373)

molecular function
	GO:0018687	biphenyl 2,3-dioxygenase activity	Catalysis of the reaction: biphenyl + NADH + H+ + O2 = (2R,3S)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+. This reaction requires Fe2+.
	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: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: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 Unit
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	Cis Peptide Bonds
		Asp B:103 - Pro B:104	[ RasMol ]
		Phe A:325 - Pro A:326	[ RasMol ]

Biological Unit
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	3gzx
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	BPHA_COMTE \| Q46372
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	BPHE_COMTE \| Q46373
		Comparative Protein Structure Models	:	ModBase
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	1.14.12.18
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UniProtKB/Swiss-Prot
	BPHA_COMTE \| Q46372	:	3gzy
	BPHE_COMTE \| Q46373	:	3gzy

3gzy	CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE FROM COMAMONAS TESTOSTERONI SP. STRAIN B-356
3gzz	CRYSTAL STRUCTURE OF THE BIPHENYL DIOXYGENASE IN COMPLEX WITH PHENYLCYCLOHEXADIENEDIOL FROM COMAMONAS TESTOSTERONI SP. STRAIN B-356

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (3, 3)

CATH Domains (2, 2)

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Gene Ontology (13, 19)

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