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Title :   STRUCTURE OF VIRAL FLAVIN-DEPENDANT THYMIDYLATE SYNTHASE THYX

Authors :   S. Graziani, J. Bernauer, S. Skouloubris, M. Graille, C. -Z. Zhou, C. Ma P. Decottignies, H. Van Tilbeurgh, H. Myllykallio, U. Liebl

Date :   17 Feb 06 (Deposition) - 16 May 06 (Release) - 17 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Fdts, Tscp, Flavin Dependent Thymidylate Synthase Fad, Flavoprotein, Nucleotide Biosynthesis, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Graziani, J. Bernauer, S. Skouloubris, M. Graille, C. -Z. Zhou, C. Marchand, P. Decottignies, H. Van Tilbeurgh, H. Myllykallio, U. Liebl
Catalytic Mechanism And Structure Of Viral Flavin- Dependent Thymidylate Synthase Thyx.
J. Biol. Chem. V. 281 24048 2006
PubMed-ID: 16707489 | Reference-DOI: 10.1074/JBC.M600745200

Molecule 1 - THYMIDYLATE SYNTHASE
	Chains	:	A
	EC Number	:	2.1.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVEX
	Expression System Strain	:	DH5[ALPHA]
	Expression System Taxid	:	668369
	Expression System Variant	:	DELTA THYA
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PARAMECIUM BURSARIA CHLORELLA VIRUS 1
	Organism Taxid	:	10506
	Synonym	:	THYX

Molecule 2 - THYMIDYLATE SYNTHASE
	Chains	:	B
	EC Number	:	2.1.1.148
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVEX
	Expression System Strain	:	DH5[ALPHA]
	Expression System Taxid	:	668369
	Expression System Variant	:	DELTA THYA
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PARAMECIUM BURSARIA CHLORELLA VIRUS 1
	Organism Taxid	:	10506
	Synonym	:	THYX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CME	4	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:54 , ARG A:78 , HIS A:79 , ARG A:80 , SER A:81 , GLN A:85 , GLU A:86 , ARG A:173 , ASP A:174 , HIS A:177 , ARG A:182 , HOH A:2047 , HOH A:2062 , HOH A:2098 , HOH A:2099 , HOH A:2100 , HOH A:2101 , HOH A:2102 , HOH A:2103 , HOH A:2104 , HOH A:2105 , HOH A:2106 , HIS B:51 , HIS B:53 , TRP B:54 , SER B:55 , ARG B:173 , FAD B:1217	BINDING SITE FOR RESIDUE FAD A1219
2	AC2	SOFTWARE	CME A:48 , HIS A:51 , HIS A:53 , TRP A:54 , SER A:55 , ARG A:173 , FAD A:1219 , HOH A:2029 , HOH A:2033 , HOH A:2035 , TRP B:54 , ARG B:78 , HIS B:79 , ARG B:80 , SER B:81 , GLN B:85 , GLU B:86 , ARG B:173 , ASP B:174 , HIS B:177 , ARG B:182 , HOH B:2054 , HOH B:2073 , HOH B:2074 , HOH B:2075	BINDING SITE FOR RESIDUE FAD B1217

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

(no "Cis Peptide Bond" information available for 2CFA)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYX	PS51331	Flavin-dependent thymidylate synthase (thyX) domain profile.	THYX_PBCV1	1-216	2	A:1-216 B:1-215

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYX	PS51331	Flavin-dependent thymidylate synthase (thyX) domain profile.	THYX_PBCV1	1-216	4	A:1-216 B:1-215

(no "Exon" information available for 2CFA)

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:180
 aligned with THYX_PBCV1 | O41156 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:217
                                                                                                                                                                                                                                                 216 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     | 
           THYX_PBCV1     1 MSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQINNKTASGLLKYCIRHKHWSIFETAFMTLELKTSRGIAAQVLRHRSFHFQEFSQRYASVMETPPPHQARFQDHKNRQNSLDTVPEDDQTWWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEFPSIAKALDWV-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee......hhhhhhhhhhhh......---.hhhhhhhh.....hhhhhhh.eeeeeeeeehhhhhhhh.....eeee...----------------------------------.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: A:1-216 UniProt: 1-216                                                                                                                                                                                       - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cfa A   1 MSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQ---KTASGLLKYcIRHKHWSIFETAFMTLELKTSRGIAAQVLRHRSFHFQEFSQ----------------------------------TWWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEFPSIAKALDWVH 217
                                    10        20        30    |   40       |50        60        70        80        |-         -         -         -   |   130       140       150       160       170       180       190       200       210       
                                                             35  39       48-CME                                   89                                124

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with THYX_PBCV1 | O41156 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
           THYX_PBCV1     1 MSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQINNKTASGLLKYCIRHKHWSIFETAFMTLELKTSRGIAAQVLRHRSFHFQEFSQRYASVMETPPPHQARFQDHKNRQNSLDTVPEDDQTWWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEFPSIAKALDW 215
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhh.eeeeeeeeehhhhhhhh.....eeee..---------.--------------------------hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh....eeeeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh-hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE THYX  PDB: B:1-215 UniProt: 1-216                                                                                                                                                                                       PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cfa B   1 MSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQINNKTASGLLKYcIRHKHWSIFETAFMTLELKTSRGIAAQVIRHRSFHFQEFS---------P--------------------------WWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEF-SIAKALDW 215
                                    10        20        30        40       |50        60        70        80       | -       | -         -         -    |  130       140       150       160       170       180       190       200     | 210     
                                                                          48-CME                                  88        98                        125                                                                              206 |       
                                                                                                                                                                                                                                         208

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 "SCOP Domain" information available for 2CFA)

(no "CATH Domain" information available for 2CFA)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (THYX_PBCV1 | O41156)

molecular function
	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:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0050797	thymidylate synthase (FAD) activity	Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP + NADPH + H+ = dTMP + tetrahydrofolate + NADP+.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006231	dTMP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0009165	nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).

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	2.1.1.148
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