1ulj

From Proteopedia

(Difference between revisions)

Current revision

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

Structural highlights

1ulj is a 6 chain structure with sequence from Rhodococcus jostii RHA1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BPHA1_RHOJR Part of the oxygenase component of the biphenyl dioxygenase system that catalyzes the stereospecific dihydroxylation of the aromatic ring of biphenyl, yielding a dihydrodiol compound. Is essential for biphenyl degradation and growth of Rhodococcus sp. strain RHA1 on biphenyl as the sole source of carbon and energy. Can also use naphtalene and 4-chlorobiphenyl (4-CB) as substrates, as well as some polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl, 2,3-dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak activity toward dibenzofuran and dibenzo-p-dioxin. Electrons are transferred from NADH to the [2Fe-2S] cluster in BphA1 via FAD of BphA4 and [2Fe-2S] cluster of BphA3.^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.

Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1.,Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M, Senda T J Mol Biol. 2004 Sep 17;342(3):1041-52. PMID:15342255^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Iwasaki T, Takeda H, Miyauchi K, Yamada T, Masai E, Fukuda M. Characterization of two biphenyl dioxygenases for biphenyl/PCB degradation in A PCB degrader, Rhodococcus sp. strain RHA1. Biosci Biotechnol Biochem. 2007 Apr;71(4):993-1002. PMID:17420585 doi:10.1271/bbb.60663
↑ Masai E, Yamada A, Healy JM, Hatta T, Kimbara K, Fukuda M, Yano K. Characterization of biphenyl catabolic genes of gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. Appl Environ Microbiol. 1995 Jun;61(6):2079-85. PMID:7793929 doi:10.1128/aem.61.6.2079-2085.1995
↑ Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M, Senda T. Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. J Mol Biol. 2004 Sep 17;342(3):1041-52. PMID:15342255 doi:10.1016/j.jmb.2004.07.062

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ulj"

@@ Line 1: / Line 1: @@
-[[Image:1ulj.gif|left|200px]]<br /><applet load="1ulj" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1ulj, resolution 2.60&Aring;" />
-'''Biphenyl dioxygenase (BphA1A2) in complex with the substrate'''<br />
-==Overview==
+==Biphenyl dioxygenase (BphA1A2) in complex with the substrate==
-Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific, dioxygenation of the aromatic ring. This enzyme has attracted the, attention of researchers due to its ability to oxidize polychlorinated, biphenyls, which is one of the serious environmental contaminants. We, determined the crystal structure of the terminal oxygenase component of, the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp., RHA1 in substrate-free and complex forms. These crystal structures, revealed that the substrate-binding pocket makes significant, conformational changes upon substrate binding to accommodate the substrate, into the pocket. Our analysis of the crystal structures suggested that the, residues in the substrate-binding pocket can be classified into three, groups, which, respectively, seem to be responsible for the catalytic, reaction, the orientation/conformation of the substrate, and the, conformational changes of the substrate-binding pocket. The cooperative, actions of residues in the three groups seem to determine the substrate, specificity of the enzyme.
+<StructureSection load='1ulj' size='340' side='right'caption='[[1ulj]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ulj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_jostii_RHA1 Rhodococcus jostii RHA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ULJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ULJ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNL:BIPHENYL'>BNL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ulj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ulj OCA], [https://pdbe.org/1ulj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ulj RCSB], [https://www.ebi.ac.uk/pdbsum/1ulj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ulj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BPHA1_RHOJR BPHA1_RHOJR] Part of the oxygenase component of the biphenyl dioxygenase system that catalyzes the stereospecific dihydroxylation of the aromatic ring of biphenyl, yielding a dihydrodiol compound. Is essential for biphenyl degradation and growth of Rhodococcus sp. strain RHA1 on biphenyl as the sole source of carbon and energy. Can also use naphtalene and 4-chlorobiphenyl (4-CB) as substrates, as well as some polychlorinated biphenyls (PCB) such as 2,2'-dichlorobiphenyl, 2,3-dichlorobiphenyl and 2,5,2'-trichlorobiphenyl. Exhibits weak activity toward dibenzofuran and dibenzo-p-dioxin. Electrons are transferred from NADH to the [2Fe-2S] cluster in BphA1 via FAD of BphA4 and [2Fe-2S] cluster of BphA3.<ref>PMID:17420585</ref> <ref>PMID:7793929</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ul/1ulj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ulj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.
-==About this Structure==
+Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1.,Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M, Senda T J Mol Biol. 2004 Sep 17;342(3):1041-52. PMID:15342255<ref>PMID:15342255</ref>
-ULJ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Rhodococcus_sp. Rhodococcus sp.] with FE2, FES and BNL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Biphenyl_2,3-dioxygenase Biphenyl 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.12.18 1.14.12.18] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1ULJ OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1., Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M, Senda T, J Mol Biol. 2004 Sep 17;342(3):1041-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15342255 15342255]
+</div>
-[[Category: Biphenyl 2,3-dioxygenase]]
+<div class="pdbe-citations 1ulj" style="background-color:#fffaf0;"></div>
-[[Category: Protein complex]]
-[[Category: Rhodococcus sp.]]
-[[Category: Fukuda, M.]]
-[[Category: Furusawa, Y.]]
-[[Category: Masai, E.]]
-[[Category: Nagarajan, V.]]
-[[Category: Senda, T.]]
-[[Category: Tanokura, M.]]
-[[Category: BNL]]
-[[Category: FE2]]
-[[Category: FES]]
-[[Category: alpha3 beta3 hetero hexamer]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:10:14 2007''
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Rhodococcus jostii RHA1]]
+[[Category: Fukuda M]]
+[[Category: Furusawa Y]]
+[[Category: Masai E]]
+[[Category: Nagarajan V]]
+[[Category: Senda T]]
+[[Category: Tanokura M]]

1ulj

From Proteopedia

Current revision

Biphenyl dioxygenase (BphA1A2) in complex with the substrate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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