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Asym./Biol. Unit (Jmol Viewer)

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Title :   REDUCED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS WITH BOUND DMSO SUBSTRATE

Authors :   A. S. Mcalpine, S. Bailey

Date :   30 Apr 97 (Deposition) - 18 Mar 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Dmso, Molybdopterin, Substrate Bound (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Mcalpine, A. G. Mcewan, S. Bailey
The High Resolution Crystal Structure Of Dmso Reductase In Complex With Dmso.
J. Mol. Biol. V. 275 613 1998
PubMed-ID: 9466935 | Reference-DOI: 10.1006/JMBI.1997.1513
(for further references see the PDB file header)

Molecule 1 - DMSO REDUCTASE
	Cellular Location	:	PERIPLASM
	Chains	:	A
	Organism Scientific	:	RHODOBACTER CAPSULATUS
	Organism Taxid	:	1061
	Strain	:	H123

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 5)

No.	Name	Count	Type	Full Name
1	4MO	1	Ligand/Ion	MOLYBDENUM(IV) ION
2	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
3	O	1	Ligand/Ion	OXYGEN ATOM
4	PGD	2	Ligand/Ion	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINEDINUCLEOTIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:114 , GLY A:115 , TRP A:116 , LYS A:117 , SER A:118 , TYR A:146 , SER A:147 , ARG A:326 , GLY A:432 , GLY A:433 , ASN A:434 , HIS A:438 , GLN A:440 , HIS A:458 , ASP A:459 , PHE A:460 , THR A:463 , ALA A:475 , ARG A:481 , ASP A:511 , ALA A:641 , HIS A:643 , HIS A:649 , SER A:650 , GLN A:651 , GLU A:715 , ASN A:737 , GLY A:754 , GLN A:755 , PGD A:783 , 4MO A:784 , O A:785 , DMS A:786 , HOH A:799 , HOH A:814 , HOH A:832 , HOH A:840	BINDING SITE FOR RESIDUE PGD A 782
2	AC2	SOFTWARE	TRP A:116 , SER A:147 , ALA A:185 , LYS A:190 , THR A:191 , GLN A:193 , ILE A:194 , ILE A:220 , ASP A:221 , PRO A:222 , VAL A:223 , THR A:225 , PRO A:240 , GLN A:241 , ASP A:243 , GLY A:321 , TRP A:322 , SER A:323 , ARG A:326 , MET A:327 , HIS A:359 , SER A:642 , HIS A:643 , PRO A:644 , PHE A:645 , ARG A:647 , LEU A:648 , HIS A:649 , GLN A:755 , PGD A:782 , 4MO A:784 , O A:785 , DMS A:786 , HOH A:801 , HOH A:813 , HOH A:824 , HOH A:854	BINDING SITE FOR RESIDUE PGD A 783
3	AC3	SOFTWARE	SER A:147 , PGD A:782 , PGD A:783 , O A:785 , DMS A:786	BINDING SITE FOR RESIDUE 4MO A 784
4	AC4	SOFTWARE	TYR A:114 , SER A:147 , PGD A:782 , PGD A:783 , 4MO A:784 , DMS A:786	BINDING SITE FOR RESIDUE O A 785
5	AC5	SOFTWARE	TYR A:114 , TRP A:116 , SER A:147 , TRP A:196 , TYR A:360 , PGD A:782 , PGD A:783 , 4MO A:784 , O A:785	BINDING SITE FOR RESIDUE DMS A 786
6	MO	UNKNOWN	SER A:147	THE SUBSTRATE DMSO IS BOUND AT THE ACTIVE SITE TO THE MOLYBDENUM, WHICH IS IN THE REDUCED (+4) STATE. THE MOLYBDENUM IS COORDINATED BY THE PTERIN SULFURS AND ANOTHER SINGLE OXYGEN.

(no "SS Bond" information available for 4DMR)

(no "Cis Peptide Bond" information available for 4DMR)

(no "SAP(SNP)/Variant" information available for 4DMR)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MOLYBDOPTERIN_PROK_2	PS00490	Prokaryotic molybdopterin oxidoreductases signature 2.	DSTOR_RHOCA	505-522	1	A:463-480
2	MOLYBDOPTERIN_PROK_3	PS00932	Prokaryotic molybdopterin oxidoreductases signature 3.	DSTOR_RHOCA	718-745	1	A:676-703

(no "Exon" information available for 4DMR)

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:773
 aligned with DSTOR_RHOCA | Q52675 from UniProtKB/Swiss-Prot  Length:823

    Alignment length:779
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814         
          DSTOR_RHOCA    45 LANGTVMSGSHWGVFTATVENGRATAFTPWEKDPHPTPMLEGVLDSIYSPTRIKYPMVRREFLEKGVNADRSTRGNGDFVRVSWDQALDLVAAEVKRVEETYGPQGVFGGSYGWKSPGRLHNCTTLLRRMLTLAGGYVNGAGDYSTGAAQVIMPHVVGTLEVYEQQTAWPVLAENTEVMVFWAADPIKTSQIGWVIPEHGAYPGLEALKAKGTKVIVIDPVRTKTVEFFGADHVTPKPQTDVAIMLGMAHTLVAEDLYDKDFIANYTSGFDKFLPYLMGETDSTPKTAEWASDISGVPAETIKELARLFISKRTMLAAGWSMQRMHHGEQAHWMLVTLASMLGQIGLPGGGFGLSYHYSGGGTPSTSGPALSGITDGGAATKGPEWLAASGASVIPVARVVDMLENPGAEFDFNGTRSKFPDVKMAYWVGGNPFVHHQDRNRMVKAWEKLETFIVHDFQWTPTARHADIVLPATTSYERNDIETIGDYSNTGILAMKKIVEPLYEARSDYDIFAAVAERLGKGKEFTEGKDEMGWIKSFYDDAAKQGKAGGVEMPAFDAFWAEGIVEFPVTDGADFVRYASFREDPLLNPLGTPTGLIEIYSKNIEKMGYDDCPAHPTWMEPLERLDGPGAKYPLHIAASHPFNRLHSQLNGTVLREGYAVQGHEPCLMHPDDAAARGIADGDVVRVHNDRGQILTGVKVTDAVMKGVIQIYEGGWYDPSDVTEPGTLDKYGDVNVLSADIGTSKLAQGNCGQTVLAEVEKYTGPAVTLTGFVAPKAAE 823
               SCOP domains d4dmra2 A:3-625 Dimethylsulfoxide reductase (DMSO reductase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   d4dmra1 A:626-781 Dimethylsulfoxide reductase (DMSO reductase)                                                                                               SCOP domains
               CATH domains --4dmrA03                     ---------------------4dmrA01 A:54-145,A:378-481,A:507-529  [code=3.40.50.740, no name defined]                   -4dmrA02 A:147-366,A:579-604 Dimethylsulfoxide Reductase, domain 2                                                                                                                                                           -----------4dm   rA01 A:   54-145,A:378-481,A:507-529  [code=3.40.50.740, no name defined]                         4dmrA03           -------4dmrA01                4dmrA03 A:5-32,A:482-499,A:530-570       --------4dmrA02                   -------4dmrA04 A:612-774  [code=2.40.40.20, no name defined]                                                                                                              ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..eeeeeeee..eeeeeee........hhhhhhhhhhh........eeehhhhhhhhh..hhh.....eee..hhhhhhhhhhhhhhhhhhh.hhh................hhhhhhhhhhhh....eee.......hhhhhhhh............hhhhhhh..eeeee...hhhhhh........hhhhhhhhhhhh..eeeee.....hhhhhh..eee......hhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhh..........hhhhhhhh...hhhhhhhhhhhhh..eeeee..hhh....hhhhhhhhhhhhhhh........eee.........................---...hhh.---..eeehhhhhhhhh....eeee..eeee.....eeeee...hhhh...hhhhhhhhhh..eeeeee....hhhhh..eeee...hhh..eeeee......eeeee............hhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhh......hhhhhhh.eee.....hhh....hhhhh..................hhhhhh...........................eee...............hhhhh.......eeee.hhhhhhh......eeeee....eeeeeeee.......eee.......................hhh.....................eeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK_3        ------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dmr A   3 LANGTVMSGSHWGVFTATVENGRATAFTPWEKDPHPSPMLAGVLDSIYSPTRIKYPMVRREFLEKGVNADRSTRGNGDFVRVSWDQALDLVAAEVKRVEETYGPSGVFGGSYGWKSPGRLHNCTTLLRRMLTLAGGYVNGAGDYSTGAAQVIMPHVVGTLEVYEQQTAWPVLAENTEVMVFWAADPIKTSQIGWVIPEHGAYPGLEALKAKGTKVIVIDPVRTKTVEFFGAEHITPKPQTDVAIMLGMAHTLVAEDLYDKDFIANYTSGFDKFLPYLDGETDSTPKTAEWAEGISGVPAETIKELARLFESKRTMLAAGWSMQRMHHGEQAHWMLVTLASMLGQIGLPGGGFGLSYHYSGGGTPSTSGPALAGITDGG---KGPEWLA---ASVIPVARVVDMLENPGAEFDFNGTRSKFPDVKMAYWVGGNPFVHHQDRNRMVKAWEKLETFVVHDFQWTPTARHADIVLPATTSYERNDIETIGDYSNTGILAMKKIVEPLYEARSDYDIFAAVAERLGKGAEFTEGKDEMGWIKSFYDDAAKQGKAAGVQMPAFDAFWAEGIVEFPVTDGADFVRYASFREDPLLNPLGTPTGLIEIYSKNIEKMGYDDCPAHPTWMEPLERLDGPGAKYPLHIAASHPFNRLHSQLNGTVLREGYAVQGHEPCLMHPDDAAARGIADGDVVRVHNDRGQILTGVKVTDAVMKGVIQIYEGGWYDPSDVTEPGTLDKYGDVNVLSADIGTSKLAQGNCGQTVLAEVEKYTGPAVTLTGFVAPKAAE 781
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       | - |     | - |     402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772         
                                                                                                                                                                                                                                                                                                                                                                                                                   380 384   390 394

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "Pfam Domain" information available for 4DMR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DSTOR_RHOCA | Q52675)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030151	molybdenum ion binding	Interacting selectively and non-covalently with molybdenum (Mo) ions.
	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:0050626	trimethylamine-N-oxide reductase (cytochrome c) activity	Catalysis of the reaction: trimethylamine + 2 (ferricytochrome c)-subunit + H2O = trimethylamine-N-oxide + 2 (ferrocytochrome c)-subunit + 2 H+.
biological process
	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.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	DSTOR_RHOCA \| Q52675	:	1dmr 1dms 1e18 1e5v 1e60 1e61 1h5n 2dmr 3dmr

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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