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Asym./Biol. Unit (Jmol Viewer)

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

Title :   THERMOSTABLE THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS

Authors :   T. J. Stout, U. Schellenberger, D. V. Santi, R. M. Stroud

Date :   09 Jul 98 (Deposition) - 16 Feb 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Methyltransferase, Dtmp Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. J. Stout, U. Schellenberger, D. V. Santi, R. M. Stroud
Crystal Structures Of A Unique Thermal-Stable Thymidylate Synthase From Bacillus Subtilis.
Biochemistry V. 37 14736 1998
PubMed-ID: 9778348 | Reference-DOI: 10.1021/BI981270L
(for further references see the PDB file header)

Molecule 1 - THYMIDYLATE SYNTHASE A
	Cell Line	:	X2913
	Chains	:	A, B
	EC Number	:	2.1.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	X2913
	Expression System Gene	:	THYA
	Expression System Plasmid	:	PTRC-THYA
	Expression System Taxid	:	562
	Expression System Vector	:	PTRC 99A
	Gene	:	THYA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		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	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:181 , ARG B:141 , ARG B:142 , HOH B:306	BINDING SITE FOR RESIDUE PO4 A 300
2	AC2	SOFTWARE	ARG A:141 , ARG A:142 , ARG B:181 , SER B:182	BINDING SITE FOR RESIDUE PO4 A 301
3	CTA	UNKNOWN	CYS A:161	CATALYTIC CYSTEINE.
4	CTB	UNKNOWN	CYS B:161	CATALYTIC CYSTEINE.

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

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

Asymmetric/Biological Unit (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TYSY1_BACSU_001 *	M	88	K	TYSY1_BACSU	---	---	A/B	M	88	K
2	UniProt	VAR_TYSY1_BACSU_002 *	S	118	N	TYSY1_BACSU	---	---	A/B	S	118	N
3	UniProt	VAR_TYSY1_BACSU_003 *	A	155	S	TYSY1_BACSU	---	---	A/B	A	155	S
4	UniProt	VAR_TYSY1_BACSU_004 *	H	171	Q	TYSY1_BACSU	---	---	A/B	H	171	Q
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMIDYLATE_SYNTHASE	PS00091	Thymidylate synthase active site.	TYSY1_BACPZ	141-169	2	A:141-169 B:141-169
1	THYMIDYLATE_SYNTHASE	PS00091	Thymidylate synthase active site.	TYSY1_BACSU	141-169	2	A:141-169 B:141-169

(no "Exon" information available for 1BSP)

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:277
 aligned with TYSY1_BACPZ | E0TVT6 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:278
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        
          TYSY1_BACPZ     2 TQFDKQYNSIIKDIMNNGISDEEFNVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVTELNKMGVHIWDQWKQEDGTIGHAYGFQLGKKNRNLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDSMALTPCVYETQWYVKQGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLFNYKHGDKLLFEVAV 279
               SCOP domains d1bspa_ A: Thymidylat e synthase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1bspA00 A:2-279 Thymi dylate Synthase, chain A                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....-................eeeee.eeeee..............hhhhhhhhhhhh......hhhhhh......hhh..........hhhhhh.eeeee..eeeehhhhhhhhhhh.......eee...hhhhhh......eeeeeeee....eeeeeee.eee...hhhhhhhhhhhhhhhhhhhh......eeeee.eeeeehhhhhhhhhhhh.......eeee......hhh..hhheeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------K-----------------------------N------------------------------------S---------------Q------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bsp A   2 TQFDKQYNSIIKDIINNGISD-EFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
                                    11        21| |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        
                                               22 |                                                                                                                                                                                                                                                               
                                                 24

Chain A from PDB  Type:PROTEIN  Length:277
 aligned with TYSY1_BACSU | P0CI79 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:278
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        
          TYSY1_BACSU     2 TQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
               SCOP domains d1bspa_ A: Thymidylat e synthase                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1bspA00 A:2-279 Thymi dylate Synthase, chain A                                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh....-................eeeee.eeeee..............hhhhhhhhhhhh......hhhhhh......hhh..........hhhhhh.eeeee..eeeehhhhhhhhhhh.......eee...hhhhhh......eeeeeeee....eeeeeee.eee...hhhhhhhhhhhhhhhhhhhh......eeeee.eeeeehhhhhhhhhhhh.......eeee......hhh..hhheeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------K-----------------------------N------------------------------------S---------------Q------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bsp A   2 TQFDKQYNSIIKDIINNGISD-EFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
                                    11        21| |     31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        
                                               22 |                                                                                                                                                                                                                                                               
                                                 24

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with TYSY1_BACPZ | E0TVT6 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:278
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        
          TYSY1_BACPZ     2 TQFDKQYNSIIKDIMNNGISDEEFNVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVTELNKMGVHIWDQWKQEDGTIGHAYGFQLGKKNRNLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDSMALTPCVYETQWYVKQGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLFNYKHGDKLLFEVAV 279
               SCOP domains d1bspb_ B: Thymidylate synthase                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1bspB00 B:2-279 Thymidylate Synthase, chain A                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....................eeeee.eeeee..............hhhhhhhhhhh.......hhhhhhh.....hhh..........hhhhh....eee..eee.hhhhhhhhhhh.......eee......hhh......eeeeeeeee..eeeeeeee.eee....hhhhhhhhhhhhhhhhhh.......eeeee.eeeeehhhhhhhhhhhh.......eeee......hhh..hhheeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------K-----------------------------N------------------------------------S---------------Q------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bsp B   2 TQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with TYSY1_BACSU | P0CI79 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:278
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        
          TYSY1_BACSU     2 TQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
               SCOP domains d1bspb_ B: Thymidylate synthase                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1bspB00 B:2-279 Thymidylate Synthase, chain A                                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....................eeeee.eeeee..............hhhhhhhhhhh.......hhhhhhh.....hhh..........hhhhh....eee..eee.hhhhhhhhhhh.......eee......hhh......eeeeeeeee..eeeeeeee.eee....hhhhhhhhhhhhhhhhhh.......eeeee.eeeeehhhhhhhhhhhh.......eeee......hhh..hhheeee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------K-----------------------------N------------------------------------S---------------Q------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bsp B   2 TQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

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: Thymidylate synthase (137)

Bacillus subtilis [TaxId: 1423] (5)

1a	d1bspa_	A:
1b	d1bspb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Thymidylate Synthase; Chain A (160)

Homologous Superfamily: Thymidylate Synthase, chain A (160)

Bacillus subtilis. Organism_taxid: 1423. Cell_line: x2913. (4)

1a	1bspA00	A:2-279
1b	1bspB00	B:2-279

(no "Pfam Domain" information available for 1BSP)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TYSY1_BACPZ | E0TVT6)

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.

Chain A,B (TYSY1_BACSU | P0CI79)

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 1bsp)

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

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (4, 4)

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