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Title :   CRYSTAL STRUCTURE OF FLAVIN-CONTAINING MONOOXYGENASE (FMO) FROM S.POMBE AND NADPH COFACTOR COMPLEX

Authors :   S. Eswaramoorthy, S. Swaminathan, S. K. Burley, New York Sgx Resear For Structural Genomics (Nysgxrc)

Date :   02 May 06 (Deposition) - 06 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Fmo, Fad, Nadph, Cofactor Complex, Oxygenase, Psi, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Eswaramoorthy, J. B. Bonanno, S. K. Burley, S. Swaminathan
Mechanism Of Action Of A Flavin-Containing Monooxygenase.
Proc. Natl. Acad. Sci. Usa V. 103 9832 2006
PubMed-ID: 16777962 | Reference-DOI: 10.1073/PNAS.0602398103

Molecule 1 - MONOOXYGENASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 14)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	GOL	2	Ligand/Ion	GLYCEROL
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
4	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:13 , GLY A:15 , PRO A:16 , SER A:17 , GLU A:38 , ARG A:39 , ARG A:40 , GLY A:45 , VAL A:46 , TRP A:47 , PRO A:83 , LEU A:84 , LEU A:88 , THR A:90 , ASN A:91 , THR A:92 , THR A:136 , ASP A:137 , VAL A:138 , CYS A:172 , ASN A:173 , GLY A:174 , TYR A:176 , PHE A:296 , PRO A:342 , PHE A:343 , NDP A:501 , HOH A:503 , HOH A:508 , HOH A:511 , HOH A:512 , HOH A:527 , HOH A:542 , HOH A:545 , HOH A:599 , HOH A:627 , HOH A:673	BINDING SITE FOR RESIDUE FAD A 500
2	AC2	SOFTWARE	GLY B:13 , GLY B:15 , PRO B:16 , SER B:17 , GLU B:38 , ARG B:39 , ARG B:40 , GLY B:45 , VAL B:46 , TRP B:47 , PRO B:83 , LEU B:84 , LEU B:88 , THR B:90 , ASN B:91 , THR B:92 , THR B:136 , ASP B:137 , VAL B:138 , CYS B:172 , ASN B:173 , GLY B:174 , TYR B:176 , PHE B:296 , PRO B:342 , PHE B:343 , NDP B:501 , HOH B:503 , HOH B:508 , HOH B:511 , HOH B:529 , HOH B:531 , HOH B:532 , HOH B:539 , HOH B:562 , HOH B:570 , HOH B:622 , HOH B:626	BINDING SITE FOR RESIDUE FAD B 500
3	AC3	SOFTWARE	TYR A:85 , GLN A:89 , ASN A:91 , TYR A:176 , GLY A:219 , ALA A:221 , SER A:222 , SER A:223 , ASP A:226 , SER A:242 , LEU A:244 , CYS A:287 , THR A:288 , FAD A:500 , HOH A:533 , HOH A:535 , HOH A:563 , HOH A:570 , HOH A:579 , HOH A:602 , HOH A:648 , HOH A:661 , HOH A:670 , HOH A:712	BINDING SITE FOR RESIDUE NDP A 501
4	AC4	SOFTWARE	TYR B:85 , GLN B:89 , ASN B:91 , TYR B:176 , GLY B:219 , ALA B:221 , SER B:222 , SER B:223 , ASP B:226 , SER B:242 , LEU B:244 , CYS B:287 , THR B:288 , GLY B:289 , FAD B:500 , HOH B:573 , HOH B:576 , HOH B:594 , HOH B:648 , HOH B:672	BINDING SITE FOR RESIDUE NDP B 501
5	AC5	SOFTWARE	TYR A:49 , SER A:51 , ARG A:86 , GLU A:206 , HOH A:509 , HOH A:653 , HOH A:654 , ASN B:48 , HOH B:636 , HOH B:641	BINDING SITE FOR RESIDUE GOL A 502
6	AC6	SOFTWARE	ASN A:48 , HOH A:585 , TYR B:49 , SER B:51 , ARG B:86 , GLU B:206 , HOH B:505 , HOH B:631 , HOH B:632 , HOH B:702	BINDING SITE FOR RESIDUE GOL B 502

(no "SS Bond" information available for 2GV8)

Asymmetric/Biological Unit

No.	Residues
1	Val A:59	-	Pro A:60
2	His A:237	-	Pro A:238
3	Tyr A:392	-	Pro A:393
4	Thr A:410	-	Pro A:411
5	Val B:59	-	Pro B:60
6	His B:237	-	Pro B:238
7	Tyr B:392	-	Pro B:393
8	Thr B:410	-	Pro B:411

(no "SAP(SNP)/Variant" information available for 2GV8)

(no "PROSITE Motif" information available for 2GV8)

(no "Exon" information available for 2GV8)

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:442
 aligned with FMO1_SCHPO | Q9HFE4 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:442
                                    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       432       442  
           FMO1_SCHPO     3 LPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVPSTNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELMGYCDQSFKPQTLQFPHRHTIQEYQRIYAQPLLPFIKLATDVLDIEKKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNIKGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLLGGGDIQNESLQQVPEITKFDPTTREIYLKGGKVLSNIDRVIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALHVVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELMFSLSGANNMYHSLDYPKDATYINKLHDWCKQATPVLEEEFPSPYWGEKERSIRENMWSIRAKFFGIE 444
               SCOP domains d2gv8a1 A:3-180,A:288-444 Flavin-dependent monoxygenase SPBP16F5.08c                                                                                                              d2gv8a2 A:181-287 Flavin-dependent monoxygenase SPBP16F5.08c                                               d2gv8a1 A:3-180,A:288-444 Flavin-dependent monoxygenase SPBP16F5.08c                                                                                          SCOP domains
               CATH domains 2gv8A01 A:3-182,A:288-444  [code=3.50.50.60, no name defined]                                                                                                                       2gv8A02 A:183-287  [code=3.50.50.60, no name defined]                                                    2gv8A01 A:3-182,A:288-444  [code=3.50.50.60, no name defined]                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhh.....eeeee.......................................................hhhhhh..............hhhhhhhhhhhhhhhhhh.ee..eeeeeeeee..eeeeeeee......eeeeee.eeee..............hhhhhhhhh...eee.hhh.hhhhhh...eeee..hhhhhhhhhhhh......eeee...........eeee..eeeee....eeee...eee....eeee.........hhhhhh.................eehhhee.....eee.......hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gv8 A   3 LPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVPSTNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELmGYCDQSFKPQTLQFPHRHTIQEYQRIYAQPLLPFIKLATDVLDIEKKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNIKGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLLGGGDIQNESLQQVPEITKFDPTTREIYLKGGKVLSNIDRVIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALHVVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELmFSLSGANNmYHSLDYPKDATYINKLHDWCKQATPVLEEEFPSPYWGEKERSIRENmWSIRAKFFGIE 444
                                    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       432|      442  
                                                                                                                         97-MSE                                                                                                                                                                                                                                                                                 377-MSE  386-MSE                                        433-MSE

Chain B from PDB  Type:PROTEIN  Length:442
 aligned with FMO1_SCHPO | Q9HFE4 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:442
                                    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       432       442  
           FMO1_SCHPO     3 LPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVPSTNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELMGYCDQSFKPQTLQFPHRHTIQEYQRIYAQPLLPFIKLATDVLDIEKKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNIKGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLLGGGDIQNESLQQVPEITKFDPTTREIYLKGGKVLSNIDRVIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALHVVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELMFSLSGANNMYHSLDYPKDATYINKLHDWCKQATPVLEEEFPSPYWGEKERSIRENMWSIRAKFFGIE 444
               SCOP domains d2gv8b1 B:3-180,B:288-444 Flavin-dependent monoxygenase SPBP16F5.08c                                                                                                              d2gv8b2 B:181-287 Flavin-dependent monoxygenase SPBP16F5.08c                                               d2gv8b1 B:3-180,B:288-444 Flavin-dependent monoxygenase SPBP16F5.08c                                                                                          SCOP domains
               CATH domains 2gv8B01 B:3-182,B:288-444  [code=3.50.50.60, no name defined]                                                                                                                       2gv8B02 B:183-287  [code=3.50.50.60, no name defined]                                                    2gv8B01 B:3-182,B:288-444  [code=3.50.50.60, no name defined]                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhh.....eeeee.......................................................hhhhhh..............hhhhhhhhhhhhhhhhhh.ee..eeeeeeeee..eeeeeeee......eeeeee.eeee..............hhhhhhhhh...eee.hhh.hhhhhh...eeee..hhhhhhhhhhhh......eeee...........eeee..eeeee....eeee...eee....eeee.........hhhhhh.................eehhhee.....eee.......hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gv8 B   3 LPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVPSTNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELmGYCDQSFKPQTLQFPHRHTIQEYQRIYAQPLLPFIKLATDVLDIEKKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNIKGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLLGGGDIQNESLQQVPEITKFDPTTREIYLKGGKVLSNIDRVIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALHVVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELmFSLSGANNmYHSLDYPKDATYINKLHDWCKQATPVLEEEFPSPYWGEKERSIRENmWSIRAKFFGIE 444
                                    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       432|      442  
                                                                                                                         97-MSE                                                                                                                                                                                                                                                                                 377-MSE  386-MSE                                        433-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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: FAD/NAD(P)-binding domain (331)

Superfamily: FAD/NAD(P)-binding domain (331)

Family: FAD/NAD-linked reductases, N-terminal and central domains (92)

Protein domain: Flavin-dependent monoxygenase SPBP16F5.08c (3)

Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] (3)

1a	d2gv8a1	A:3-180,A:288-444
1b	d2gv8a2	A:181-287
1c	d2gv8b1	B:3-180,B:288-444
1d	d2gv8b2	B:181-287

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Fission yeast (Schizosaccharomyces pombe) (3)

1a	2gv8A02	A:183-287
1b	2gv8B02	B:183-287
1c	2gv8A01	A:3-182,A:288-444
1d	2gv8B01	B:3-182,B:288-444

(no "Pfam Domain" information available for 2GV8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FMO1_SCHPO | Q9HFE4)

molecular function
	GO:0004499	N,N-dimethylaniline monooxygenase activity	Catalysis of the reaction: N,N-dimethylaniline + NADPH + H+ + O2 = N,N-dimethylaniline N-oxide + NADP+ + H2O.
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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.
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.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
cellular component
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		His A:237 - Pro A:238	[ RasMol ]
		His B:237 - Pro B:238	[ RasMol ]
		Thr A:410 - Pro A:411	[ RasMol ]
		Thr B:410 - Pro B:411	[ RasMol ]
		Tyr A:392 - Pro A:393	[ RasMol ]
		Tyr B:392 - Pro B:393	[ RasMol ]
		Val A:59 - Pro A:60	[ RasMol ]
		Val B:59 - Pro B:60	[ RasMol ]

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	2gv8
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	FMO1_SCHPO \| Q9HFE4	:	1vqw 2gvc

1vqw	WILD TYPE STRUCTURE OF FMO
2gvc	RELATED ID: NYSGXRC-T1729 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

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