1B02 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE A FROM BACILLUS SUBTILIS

Authors :   K. M. Fox, F. Maley, A. Garibian, L. Changchien, P. Vanroey

Date :   16 Nov 98 (Deposition) - 29 Mar 99 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

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

Reference :   K. M. Fox, F. Maley, A. Garibian, L. M. Changchien, P. Van Roey
Crystal Structure Of Thymidylate Synthase A From Bacillus Subtilis.
Protein Sci. V. 8 538 1999
PubMed-ID: 10091656

Molecule 1 - PROTEIN (THYMIDYLATE SYNTHASE)
	Chains	:	A
	EC Number	:	2.1.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET17XB
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	C2F	1	Ligand/Ion	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID
2	UFP	1	Ligand/Ion	5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:28 , TYR A:108 , CYS A:161 , ARG A:181 , SER A:182 , ASN A:183 , ASP A:184 , GLY A:188 , ASN A:192 , HIS A:222 , TYR A:224 , C2F A:281 , HOH A:291 , HOH A:313	BINDING SITE FOR RESIDUE UFP A 280
2	AC2	SOFTWARE	ALA A:64 , THR A:67 , ILE A:93 , TRP A:94 , TRP A:97 , ASP A:184 , GLY A:188 , ALA A:278 , UFP A:280 , HOH A:299 , HOH A:332 , HOH A:342 , HOH A:351 , HOH A:360	BINDING SITE FOR RESIDUE C2F A 281

(no "SS Bond" information available for 1B02)

(no "Cis Peptide Bond" information available for 1B02)

Asymmetric/Biological Unit (4, 4)

								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	M	88	K
2	UniProt	VAR_TYSY1_BACSU_002 *	S	118	N	TYSY1_BACSU	---	---	A	S	118	N
3	UniProt	VAR_TYSY1_BACSU_003 *	A	155	S	TYSY1_BACSU	---	---	A	A	155	S
4	UniProt	VAR_TYSY1_BACSU_004 *	H	171	Q	TYSY1_BACSU	---	---	A	H	171	Q
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 1)

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

(no "Exon" information available for 1B02)

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

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
          TYSY1_BACPZ     1 MTQFDKQYNSIIKDIMNNGISDEEFNVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVTELNKMGVHIWDQWKQEDGTIGHAYGFQLGKKNRNLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDSMALTPCVYETQWYVKQGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLFNYKHGDKLLFEVAV 279
               SCOP domains d1b02a_ A: Thymidylate synthase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1b02A00 A:1-279 Thymidylate Synthase, chain A                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....................eeeee.eeeee..............hhhhhhhhhhhh......hhhhhh......hhh..........hhhhhh.eeee....eeehhhhhhhhhhh.......eee......hhh......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
                 1b02 A   1 MTQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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

    Alignment length:279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
          TYSY1_BACSU     1 MTQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
               SCOP domains d1b02a_ A: Thymidylate synthase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1b02A00 A:1-279 Thymidylate Synthase, chain A                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....................eeeee.eeeee..............hhhhhhhhhhhh......hhhhhh......hhh..........hhhhhh.eeee....eeehhhhhhhhhhh.......eee......hhh......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
                 1b02 A   1 MTQFDKQYNSIIKDIINNGISDEEFDVRTKWDSDGTPAHTLSVISKQMRFDNSEVPILTTKKVAWKTAIKELLWIWQLKSNDVNDLNMMGVHIWDQWKQEDGTIGHAYGFQLGKKNRSLNGEKVDQVDYLLHQLKNNPSSRRHITMLWNPDELDAMALTPCVYETQWYVKHGKLHLEVRARSNDMALGNPFNVFQYNVLQRMIAQVTGYELGEYIFNIGDCHVYTRHIDNLKIQMEREQFEAPELWINPEVKDFYDFTIDDFKLINYKHGDKLLFEVAV 279
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

d1b02a_

Asymmetric/Biological Unit

Classes(

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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. Strain: 168. (1)

1b02A00

A:1-279

(no "Pfam Domain" information available for 1B02)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain A (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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1B02)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

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Exons (0, 0)

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