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Asym./Biol. Unit (Jmol Viewer)

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

Title :   THYMIDYLATE SYNTHASE FROM STAPHYLOCOCCUS AUREUS.

Authors :   J. Osipiuk, J. Holowicki, R. Jedrzejczak, E. Rubin, K. Guinn, T. Ioerge D. Baker, J. Sacchettini, A. Joachimiak, Midwest Center For Struc Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susce To Known Mtb Inhibitors (Mtbi)

Date :   14 Feb 12 (Deposition) - 21 Mar 12 (Release) - 21 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

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

Keywords :   Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi, Thymidylate Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Osipiuk, J. Holowicki, R. Jedrzejczak, E. Rubin, K. Guinn, T. Ioerger, D. Baker, J. Sacchettini, A. Joachimiak
Thymidylate Synthase From Staphylococcus Aureus.
To Be Published
PubMed: search

Molecule 1 - THYMIDYLATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.1.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SAV1427, THYA
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	158878
	Strain	:	SUBSP. AUREUS MU50
	Synonym	:	TS, TSASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	UMP	2	Ligand/Ion	2'-DEOXYURIDINE 5'-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:26 , CYS A:201 , HIS A:202 , GLN A:220 , ARG A:221 , SER A:222 , ALA A:223 , ASP A:224 , ASN A:232 , HIS A:262 , TYR A:264 , ARG B:181 , ARG B:182	BINDING SITE FOR RESIDUE UMP A 501
2	AC2	SOFTWARE	ARG A:181 , ARG A:182 , ARG B:26 , CYS B:201 , HIS B:202 , GLN B:220 , ARG B:221 , SER B:222 , ALA B:223 , ASP B:224 , ASN B:232 , HIS B:262 , TYR B:264	BINDING SITE FOR RESIDUE UMP B 501

(no "SS Bond" information available for 4DQ1)

(no "Cis Peptide Bond" information available for 4DQ1)

(no "SAP(SNP)/Variant" information available for 4DQ1)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_SYNTHASE	PS00091	Thymidylate synthase active site.	TYSY_STAAM	181-209	2	A:181-209 B:181-209

(no "Exon" information available for 4DQ1)

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:312
 aligned with TYSY_STAAM | P67046 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:312
                                    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  
           TYSY_STAAM     3 NSFDAAYHSLCEEVLEIGNTRNDRTNTGTISKFGHQLRFDLSKGFPLLTTKKVSFKLVATELLWFIKGDTNIQYLLKYNNNIWNEWAFENYIKSDEYNGPDMTDFGHRALSDPEFNEQYKEQMKQFKQRILEDDTFAKQFGDLGNVYGKQWRDWVDKDGNHFDQLKTVIEQIKHNPDSRRHIVSAWNPTEIDTMALPPCHTMFQFYVQDGKLSCQLYQRSADIFLGVPFNIASYALLTHLIAKECGLEVGEFVHTFGDAHIYSNHIDAIQTQLARESFNPPTLKINSDKSIFDINYEDLEIVDYESHPAIKA 314
               SCOP domains d4dq1a_ A: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhh.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhh........eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhhh......eeee....hhhhhhhh.eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dq1 A   3 NSFDAAYHSLCEEVLEIGNTRNDRTNTGTISKFGHQLRFDLSKGFPLLTTKKVSFKLVATELLWFIKGDTNIQYLLKYNNNIWNEWAFENYIKSDEYNGPDMTDFGHRALSDPEFNEQYKEQMKQFKQRILEDDTFAKQFGDLGNVYGKQWRDWVDKDGNHFDQLKTVIEQIKHNPDSRRHIVSAWNPTEIDTMALPPCHTMFQFYVQDGKLSCQLYQRSADIFLGVPFNIASYALLTHLIAKECGLEVGEFVHTFGDAHIYSNHIDAIQTQLARESFNPPTLKINSDKSIFDINYEDLEIVDYESHPAIKA 314
                                    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

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with TYSY_STAAM | P67046 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:312
                                    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  
           TYSY_STAAM     3 NSFDAAYHSLCEEVLEIGNTRNDRTNTGTISKFGHQLRFDLSKGFPLLTTKKVSFKLVATELLWFIKGDTNIQYLLKYNNNIWNEWAFENYIKSDEYNGPDMTDFGHRALSDPEFNEQYKEQMKQFKQRILEDDTFAKQFGDLGNVYGKQWRDWVDKDGNHFDQLKTVIEQIKHNPDSRRHIVSAWNPTEIDTMALPPCHTMFQFYVQDGKLSCQLYQRSADIFLGVPFNIASYALLTHLIAKECGLEVGEFVHTFGDAHIYSNHIDAIQTQLARESFNPPTLKINSDKSIFDINYEDLEIVDYESHPAIKA 314
               SCOP domains d4dq1b_ B: automated matches                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh....hhhhhhh....hhhhhhhhhh..........------------.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhee.....eehhhhhhhhhhhhh......eee...............eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee.........hhh.eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dq1 B   3 NSFDAAYHSLCEEVLEIGNTRNDRTNTGTISKFGHQLRFDLSKGFPLLTTKKVSFKLVATELLWFIKGDTNIQYLLKYNNNIWNEWAFENYIKSDEYNGPDM------------FNEQYKEQMKQFKQRILEDDTFAKQFGDLGNVYGKQWRDWVDKDGNHFDQLKTVIEQIKHNPDSRRHIVSAWNPTEIDTMALPPCHTMFQFYVQDGKLSCQLYQRSADIFLGVPFNIASYALLTHLIAKECGLEVGEFVHTFGDAHIYSNHIDAIQTQLARESFNPPTLKINSDKSIFDINYEDLEIVDYESHPAIKA 314
                                    12        22        32        42        52        62        72        82        92       102 |       -    |  122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
                                                                                                                               104          117

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) (23004)

Fold: Thymidylate synthase/dCMP hydroxymethylase (193)

Superfamily: Thymidylate synthase/dCMP hydroxymethylase (193)

Family: Thymidylate synthase/dCMP hydroxymethylase (183)

Protein domain: automated matches (38)

Staphylococcus aureus [TaxId: 158878] (1)

1a	d4dq1a_	A:
1b	d4dq1b_	B:

(no "CATH Domain" information available for 4DQ1)

(no "Pfam Domain" information available for 4DQ1)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TYSY_STAAM | P67046)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0004799	thymidylate synthase activity	Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
	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:0006235	dTTP biosynthetic process	The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
	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).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dq1)

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	4dq1
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	TYSY_STAAM \| P67046
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	2.1.1.45
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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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