1YW1 - JenaLib

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Title :   STRUCTURE OF YTNJ FROM BACILLUS SUBTILIS IN COMPLEX WITH FMN

Authors :   S. K. Burley, New York Sgx Research Center For Structural Genom (Nysgxrc)

Date :   16 Feb 05 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.81

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

Keywords :   Nysgxrc, Beta-Alpha Barrel, Fmn, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Gorman, L. Shapiro
Structure Of Ytnj From Bacillus Subtilis In Complex With Fm
To Be Published
PubMed: search

Molecule 1 - PROTEIN YTNJ
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	MODIFIED PET28B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	YTNJ
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	NITRILOTRIACETATE MONOOXYGENASE COMPONENT A HOMOLOG YTNJ

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	FMN	1	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
2	GLC	2	Ligand/Ion	ALPHA-D-GLUCOSE
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:14 , ALA A:57 , ASP A:58 , GLY A:59 , PHE A:70 , ARG A:73 , GLN A:130 , FMN A:2606 , HOH A:2645 , HOH A:2651 , HOH A:2663	BINDING SITE FOR RESIDUE GLC A 2605
2	AC2	SOFTWARE	ALA A:57 , ASP A:58 , THR A:95 , PRO A:129 , GLN A:130 , HIS A:145 , TYR A:149 , ALA A:217 , GLY A:218 , SER A:219 , SER A:220 , PHE A:235 , THR A:236 , HIS A:237 , GLC A:2605	BINDING SITE FOR RESIDUE FMN A 2606

(no "SS Bond" information available for 1YW1)

Asymmetric Unit

No.	Residues
1	Gly A:200	-	Pro A:201

(no "SAP(SNP)/Variant" information available for 1YW1)

(no "PROSITE Motif" information available for 1YW1)

(no "Exon" information available for 1YW1)

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:393
 aligned with MOXC_BACSU | O34974 from UniProtKB/Swiss-Prot  Length:442

    Alignment length:429
                                    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       382       392       402       412       422         
           MOXC_BACSU     3 RADFIQFGAMIHGVGGTTDGWRHPDVDPSASTNIEFYMKKAQTAEKGLFSFIFIADGLFISEKSIPHFLNRFEPITILSALASVTKNIGLVGTFSTSFTEPFTISRQLMSLDHISGGRAGWNLVTSPQEGAARNHSKSNLPEHTERYEIAQEHLDVVRGLWNSWEHDAFIHNKKTGQFFDQAKLHRLNHKGKYFQVEGPLNIGRSKQGEPVVFQAGSSETGRQFAAKNADAIFTHSNSLEETKAFYADVKSRAADEGRDPSSVRIFPGISPIVADTEEEAEKKYREFAELIPIENAVTYLARFFDDYDLSVYPLDEPFPDIGDVGKNAFQSTTDRIKREAKARNLTLREVAQEMAFPRTLFIGTPERVASLIETWFNAEAADGFIVGSDIPGTLDAFVEKVIPILQERGLYRQDYRGGTLRENLGLGIP 431
               SCOP domains d1yw1a_ A: Putative monooxygenase YtnJ                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1yw1A00 A:3-431 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------Bac_luciferase-1yw1A01 A:15-385                                                                                                                                                                                                                                                                                                                                                    ---------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee........hhhhh.....hhhhhhhhhhhhhhhhhhh...eeee..........hhhhhh..hhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhh........hhhhhhhhhhhhhhhhhhhhh.................hhhhh....ee....ee..............eeee...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhh...hhhhheeeeee..ee..hhhhhhhhhhhhhh..hhhhhhhhhh.------------------------------------.......hhhhhhhhhhh.....eehhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh..........hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yw1 A   3 RADFIQFGAmIHGVGGTTDGWRHPDVDPSASTNIEFYmKKAQTAEKGLFSFIFIADGLFISEKSIPHFLNRFEPITILSALASVTKNIGLVGTFSTSFTEPFTISRQLmSLDHISGGRAGWNLVTSPQEGAARNHSKSNLPEHTERYEIAQEHLDVVRGLWNSWEHDAFIHNKKTGQFFDQAKLHRLNHKGKYFQVEGPLNIGRSKQGEPVVFQAGSSETGRQFAAKNADAIFTHSNSLEETKAFYADVKSRAADEGRDPSSVRIFPGISPIVADTEEEAEKKYREFAELIPIENAVTYLAR------------------------------------EAKARNLTLREVAQEmAFPRTLFIGTPERVASLIETWFNAEAADGFIVGSDIPGTLDAFVEKVIPILQERGLYRQDYRGGTLRENLGLGIP 431
                                    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 |       -         -         -       342       352   |   362       372       382       392       402       412       422         
                                    12-MSE                      40-MSE                                                                111-MSE                                                                                                                                                                                          304                                  341            356-MSE

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Bacterial luciferase-like (24)

Family: Ssud-like monoxygenases (4)

Protein domain: Putative monooxygenase YtnJ (2)

Bacillus subtilis [TaxId: 1423] (2)

d1yw1a_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: FMN dependent fluorescent proteins (19)

Bacillus subtilis. Organism_taxid: 1423. (2)

1yw1A00

A:3-431

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Bac_luciferase] (10)

Family: Bac_luciferase (10)

Bacillus subtilis (2)

Bac_luciferase-1yw1A01

A:15-385

Asymmetric Unit(hide GO term definitions)

Chain A (MOXC_BACSU | O34974)

molecular function
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	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.
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.

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Biological Unit
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	MOXC_BACSU \| O34974	:	1tvl

1tvl	THE SAME PROTEIN WITHOUT FMN RELATED ID: NYSGXRC-T773 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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