2VET - JenaLib

Title :   CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH DUMP

Authors :   R. R. Sotelo-Mundo, R. Arreola, F. Maley, W. R. Montfort

Date :   26 Oct 07 (Deposition) - 04 Dec 07 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Repressor, Cytoplasm, Rna-Binding, Transferase, Nucleotide Biosynthesis, Dump Substrate, Methyltransferase, Thymidylate Synthase, Translation Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. A. Arvizu-Flores, R. Sugich-Miranda, R. Arreola, K. D. Garcia-Orozco, E. F. Velazquez-Contreras, W. R. Montfort, F. Maley, R. R. Sotelo-Mundo
Role Of An Invariant Lysine Residue In Folate Binding On Escherichia Coli Thymidylate Synthase: Calorimetric And Crystallographic Analysis Of The K48Q Mutant.
Int. J. Biochem. Cell Biol. V. 40 2206 2008
PubMed-ID: 18403248 | Reference-DOI: 10.1016/J.BIOCEL.2008.02.025

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 (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:264
 aligned with TYSY_ECOLI | P0A884 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:264
                                    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    
           TYSY_ECOLI     1 MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
               SCOP domains d2veta_ A: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2vetA00 A:1-264 Thymidylate Synthase, chain A                                                                                                                                                                                                                            CATH domains
               Pfam domains Thymidylat_synt-2vetA01 A:1-264                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh...hhhhhhh.................hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vet A   1 MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTQRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                                    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

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (TYSY_ECOLI | P0A884)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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).
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1aiq	CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT
1ajm	CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT
1an5	E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717
1aob	E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DDURD
1axw	E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND 2'-DEOXYURIDINE 5'- MONOPHOSPHATE (DUMP)
1bdu	E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DURD
1bid	E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DUMP
1bjg	D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING
1bq1	E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5 '-MONOPHOSPHATE (DUMP)
1bq2	E. COLI THYMIDYLATE SYNTHASE MUTANT N177A
1ddu	E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'- DIDEOXYURIDINE (DDURD)
1dna	D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING
1ev5	CRYSTAL STRUCTURE ANALYSIS OF ALA167 MUTANT OF ESCHERICHIA COLI
1ev8	CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI
1evf	CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI
1evg	CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI WITH UNMODIFIED CATALYTIC CYSTEINE
1f4b	CRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE
1f4c	CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASECOVALENTLY MODIFIED AT C146 WITH N-[ TOSYL-D-PROLINYL]AMINO-ETHANETHIOL
1f4d	CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE C146S,L143C COVALENTLY MODIFIED AT C143 WITH N-[TOSYL-D-PROLINYL]AMINO- ETHANETHIOL
1f4e	CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXEDWITH TOSYL-D-PROLINE
1f4f	CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXEDWITH SP- 722
1f4g	CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXEDWITH SP- 876
1ffl	CRYSTAL STRUCTURE OF THE APO-THYMIDYLATE SYNTHASE R166QMUTANT
1fwm	CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE R166Q MUTANT
1jg0	CRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASECOMPLEXED WITH 2'- DEOXYURIDINE-5'-MONOPHOSPHATE AND N,O- DIDANSYL-L-TYROSINE
1jtq	E. COLI TS COMPLEX WITH DUMP AND THE PYRROLO(2,3-D)PYRIMIDINE-BASED ANTIFOLATE LY341770
1jtu	E. COLI THYMIDYLATE SYNTHASE IN A COMPLEX WITH DUMP ANDLY338913, A POLYGLUTAMYLATED PYRROLO(2,3-D)PYRIMIDINE-BASED ANTIFOLATE
1jut	E. COLI THYMIDYLATE SYNTHASE BOUND TO DUMP AND LY338529, APYRROLO(2, 3-D)PYRIMIDINE- BASED ANTIFOLATE
1kce	E. COLI THYMIDYLATE SYNTHASE MUTANT E58Q IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5 '-MONOPHOSPHATE (DUMP)
1kzi	CRYSTAL STRUCTURE OF ECTS/DUMP/THF COMPLEX
1kzj	CRYSTAL STRUCTURE OF ECTS W80G/DUMP/CB3717 COMPLEX
1nce	CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLITHYMIDYLATE SYNTHASE D169C WITH DUMP AND THE ANTIFOLATECB3717
1qqq	CRYSTAL STRUCTURE ANALYSIS OF SER254 MUTANT OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE
1syn	E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH BW1843U89 AND 2'- DEOXYURIDINE 5'- MONOPHOSPHATE (DUMP)
1tdu	E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'- DEOXYURIDINE (DURD)
1tjs	E. COLI THYMIDYLATE SYNTHASE
1tlc	THYMIDYLATE SYNTHASE COMPLEXED WITH DGMP AND FOLATE ANALOG 1843U89
1tls	THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE
1trg	E. COLI THYMIDYLATE SYNTHASE IN SYMMETRIC COMPLEX WITH CB3717 AND 2' -DEOXYURIDINE 5'- MONOPHOSPHATE (DUMP)
1tsd	THYMIDYLATE SYNTHASE COMPLEX WITH 2'- DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) AND FOLATE ANALOG 1843U89
1tsn	THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND METHYLENETETRAHYDROFOLATE
1tys	THYMIDYLATE SYNTHASE MUTANT WITH CYS 146 REPLACED BY SER (C146S)
1zpr	E. COLI THYMIDYLATE SYNTHASE MUTANT E58Q IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5 '-MONOPHOSPHATE (DUMP)
2a9w	E. COLI TS COMPLEXED WITH DUMP AND INHIBITOR GA9
2bbq	THYMIDYLATE SYNTHASE COMPLEX WITH D-UMP AND POLYGLUTAMYL CB3717
2ftn	E. COLI THYMIDYLATE SYNTHASE Y94F MUTANT
2fto	Y94F MUTANT OF THYMIDYLATE SYNTHASE BOUND TO THYMIDINE-5'-PHOSPHATE AND 10-PROPARGYL-5 ,8-DIDEAZAFOLID ACID
2ftq	E. COLI THYMIDYLATE SYNTHASE AT 1.8 A RESOLUTION
2g8m	ESCHERICHIA COLI THYMIDYLATE SYNTHASE Y209W IN COMPLEX WITHSUBSTRATE, DUMP, AND A COFACTOR ANALOG, CB3717
2g8o	HIGH RESOLUTION STRUCTURE OF ESCHERICHIA COLI THYMIDYLATESYNTHASE TERNARY COMPLEX WITH DUMP AND A COFACTOR ANALOG,CB3717
2g8x	ESCHERICHIA COLI Y209W APOPROTEIN
2kce	BINDING OF THE ANTICANCER DRUG ZD1694 TO E . COLI THYMIDYLATE SYNTHASE: ASSESSING SPECIFICITY AND AFFINITY
2tsc	THYMIDYLATE SYNTHASE COMPLEX WITH DUMP AND AN ANTI-FOLATE (CB3717)
2vf0	CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH 5NO2DUMP AND BW1843U89
3b5b	CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q MUTANT K48Q COMPLEXED WITH 5NO2DUMP
3tms	THYMIDYLATE SYNTHASE

Description