1TMO - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA

Authors :   M. Czjzek, J. P. Dos Santos, G. Giordano, V. Mejean

Date :   03 Aug 98 (Deposition) - 30 Mar 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Tmao Reductase, Oxotransferase, Molybdoenzyme, Mo-Cofactor, Molybdenum, Bis (Molybdopterin Guanine Dinucleotide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Czjzek, J. P. Dos Santos, J. Pommier, G. Giordano, V. Mejean, R. Haser
Crystal Structure Of Oxidized Trimethylamine N-Oxide Reductase From Shewanella Massilia At 2. 5 A Resolution.
J. Mol. Biol. V. 284 435 1998
PubMed-ID: 9813128 | Reference-DOI: 10.1006/JMBI.1998.2156
(for further references see the PDB file header)

Molecule 1 - TRIMETHYLAMINE N-OXIDE REDUCTASE
	Cellular Location	:	PERIPLASM
	Chains	:	A
	EC Number	:	1.6.6.9
	Organism Scientific	:	SHEWANELLA MASSILIA
	Organism Taxid	:	76854
	Other Details	:	MARINE BACTERIA, ISOLATED FROM THE FISH MULLUS SURMULETUS
	Synonym	:	TMAO REDUCTASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	2MD	2	Ligand/Ion	GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER
2	2MO	1	Ligand/Ion	MOLYBDENUM (IV)OXIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:117 , TRP A:118 , ALA A:120 , SER A:127 , SER A:149 , ARG A:332 , GLY A:441 , ASN A:442 , ASN A:443 , ASN A:446 , HIS A:447 , VAL A:467 , ASP A:468 , THR A:472 , ALA A:484 , ARG A:490 , ASP A:520 , SER A:649 , HIS A:651 , LEU A:656 , HIS A:657 , SER A:658 , GLN A:659 , ASN A:753 , TYR A:771 , 2MD A:800 , 2MO A:801 , HOH A:869 , HOH A:870	BINDING SITE FOR RESIDUE 2MD A 799
2	AC2	SOFTWARE	SER A:149 , SER A:187 , LYS A:192 , ASN A:193 , VAL A:196 , ILE A:226 , ASP A:227 , THR A:231 , GLN A:247 , ASP A:249 , TRP A:328 , CYS A:329 , ARG A:332 , GLN A:333 , TRP A:646 , GLN A:648 , CYS A:650 , HIS A:651 , PRO A:652 , ARG A:655 , HIS A:657 , 2MD A:799 , 2MO A:801 , HOH A:902	BINDING SITE FOR RESIDUE 2MD A 800
3	AC3	SOFTWARE	TRP A:118 , SER A:149 , 2MD A:799 , 2MD A:800	BINDING SITE FOR RESIDUE 2MO A 801
4	MOS	UNKNOWN	2MD A:799 , 2MD A:800 , 2MO A:801 , SER A:149	MOLYBDENUM COFACTOR BINDING THE MOLYBDENUM ION, ALSO LIGATED BY TWO OXO GROUPS AND OG FROM SER 149.

(no "SS Bond" information available for 1TMO)

(no "Cis Peptide Bond" information available for 1TMO)

(no "SAP(SNP)/Variant" information available for 1TMO)

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.	TORA_SHEMA	503-520	1	A:472-489
2	MOLYBDOPTERIN_PROK_3	PS00932	Prokaryotic molybdopterin oxidoreductases signature 3.	TORA_SHEMA	716-743	1	A:685-712

(no "Exon" information available for 1TMO)

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:794
 aligned with TORA_SHEMA | O87948 from UniProtKB/Swiss-Prot  Length:829

    Alignment length:794
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825    
           TORA_SHEMA    36 NEDEWLTTGSHFGAFKMKRKNGVIAEVKPFDLDKYPTDMINGIRGMVYNPSRVRYPMVRLDFLLKGHKSNTHQRGDFRFVRVTWDKALTLFKHSLDEVQTQYGPSGLHAGQTGWRATGQLHSSTSHMQRAVGMHGNYVKKIGDYSTGAGQTILPYVLGSTEVYAQGTSWPLILEHSDTIVLWSNDPYKNLQVGWNAETHESFAYLAQLKEKVKQGKIRVISIDPVVTKTQAYLGCEQLYVNPQTDVTLMLAIAHEMISKKLYDDKFIQGYSLGFEEFVPYVMGTKDGVAKTPEWAAPICGVEAHVIRDLAKTLVKGRTQFMMGWCIQRQQHGEQPYWMAAVLATMIGQIGLPGGGISYGHHYSSIGVPSSGAAAPGAFPRNLDENQKPLFDSSDFKGASSTIPVARWIDAILEPGKTIDANGSKVVYPDIKMMIFSGNNPWNHHQDRNRMKQAFHKLECVVTVDVNWTATCRFSDIVLPACTTYERNDIDVYGAYANRGILAMQKMVEPLFDSLSDFEIFTRFAAVLGKEKEYTRNMGEMEWLETLYNECKAANAGKFEMPDFATFWKQGYVHFGDGEVWTRHADFRNDPEINPLGTPSGLIEIFSRKIDQFGYDDCKGHPTWMEKTERSHGGPGSDKHPIWLQSCHPDKRLHSQMCESREYRETYAVNGREPVYISPVDAKARGIKDGDIVRVFNDRGQLLAGAVVSDNFPKGIVRIHEGAWYGPVGKDGSTEGGAEVGALCSYGDPNTLTLDIGTSKLAQACSAYTCLVEFEKYQGKVPKVSSFDGPIEVEI 829
               SCOP domains d1tmoa2 A:5-631 Trimethylamine N-oxide reductase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   d1tmoa1 A:632-798 Trimethylamine N-oxide reductase                                                                                                                      SCOP domains
               CATH domains --1tmoA03                     ---------------------1tmoA01 A:56-147,A:384-490,A:516-538  [code=3.40.50.740, no name defined]                   -1tmoA02 A:149-372,A:585-610 Dimethylsulfoxide Reductase, domain 2                                                                                                                                                               -----------1tmoA01 A:56-147,A:384-490,A:516-538  [code=3.40.50.740, no name defined]                                  1tmoA03           -------1tmoA01                1tmoA03 A:7-34,A:491-508,A:539-578      ------1tmoA02                   -------1tmoA04 A:618-790  [code=2.40.40.20, no name defined]                                                                                                                        -------- CATH domains
               Pfam domains ---------------------------------------------------Molybdopterin-1tmoA02 A:56-530                                                                                                                                                                                                                                                                                                                                                                                                                                                             ------------------------------------------------------------------------------------------------------------------Molydop_binding-1tmoA01 A:645-774                                                                                                 ------------------------ Pfam domains
         Sec.struct. author .....eeeee..eeeeeeee..eeeeeee........hhhh.hhhhh.........eeehhhhhhhhh..hhh.....eee..hhhhhhhhhhhhhhhhhh..hhh................hhhhhhhhhh......eee.......hhhhhhhh............hhhhhhh..eeeee...hhhh..........hhhhhhhhhhhhhhh...eeeee.....hhhhhh..eee......hhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhh.........hhhhhhhh...hhhhhhhhhhhhh..eeeee..hhh.....hhhhhhhhhhhhhh........eee...........................................eeehhhhhhhhh....eee....eee.....eeeee...hhhh...hhhhhhhhhh..eeeeee....hhhhh..eeee...hhh..eeeee......eeeee............hhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhh.eee..........hhhhh..................hhhhhh.............................eee...............hhhhhh.......eeee.hhhhhhh......eeeeee..eeeeeeeee.......eee................hhhh..........hhh.....................eeee................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MOLYBDOPTERIN_PROK_3        -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmo A   5 NEDEWLTTGSHFGAFKMKRKNGVIAEVKPFDLDKYPTDMINGIRGMVYNPSRVRYPMVRLDFLLKGHKSNTHQRGDFRFVRVTWDKALTLFKHSLDEVQTQYGPSGLHAGQTGWRATGQLHSSTSHMQRAVGMHGNYVKKIGDYSTGAGQTILPYVLGSTEVYAQGTSWPLILEHSDTIVLWSNDPYKNLQVGWNAETHESFAYLAQLKEKVKQGKIRVISIDPVVTKTQAYLGCEQLYVNPQTDVTLMLAIAHEMISKKLYDDKFIQGYSLGFEEFVPYVMGTKDGVAKTPEWAAPICGVEAHVIRDLAKTLVKGRTQFMMGWCIQRQQHGEQPYWMAAVLATMIGQIGLPGGGISYGHHYSSIGVPSSGAAAPGAFPRNLDENQKPLFDSSDFKGASSTIPVARWIDAILEPGKTIDANGSKVVYPDIKMMIFSGNNPWNHHQDRNRMKQAFHKLECVVTVDVNWTATCRFSDIVLPACTTYERNDIDVYGAYANRGILAMQKMVEPLFDSLSDFEIFTRFAAVLGKEKEYTRNMGEMEWLETLYNECKAANAGKFEMPDFATFWKQGYVHFGDGEVWTRHADFRNDPEINPLGTPSGLIEIFSRKIDQFGYDDCKGHPTWMEKTERSHGGPGSDKHPIWLQSCHPDKRLHSQMCESREYRETYAVNGREPVYISPVDAKARGIKDGDIVRVFNDRGQLLAGAVVSDNFPKGIVRIHEGAWYGPVGKDGSTEGGAEVGALCSYGDPNTLTLDIGTSKLAQACSAYTCLVEFEKYQGKVPKVSSFDGPIEVEI 798
                                    14        24        34        44        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

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AcetylDC-like (37)

Family: Molydop_binding (24)

Shewanella massilia (1)

Molydop_binding-1tmoA01

A:645-774

Clan: no clan defined [family: Molybdopterin] (24)

Family: Molybdopterin (24)

Shewanella massilia (1)

Molybdopterin-1tmoA02

A:56-530

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TORA_SHEMA | O87948)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		2MD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		2MO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		MOS	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tmo)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1tmo
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TORA_SHEMA \| O87948
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.6.6.9
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TORA_SHEMA \| O87948
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1TMO)

(no "Related Entries Specified in the PDB File" available for 1TMO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (4, 4)

Pfam Domains (2, 2)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File