2G8X - JenaLib

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Title :   ESCHERICHIA COLI Y209W APOPROTEIN

Authors :   T. T. Lee, J. S. Finer-Moore, R. M. Stroud

Date :   03 Mar 06 (Deposition) - 14 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.83

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

Keywords :   Beta Sheet, Alpha/Beta Protein, Dtt, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Newby, T. T. Lee, R. J. Morse, L. Liu, Y. Liu, P. Venkatraman, D. V. Santi, J. S. Finer-Moore, R. M. Stroud
The Role Of Protein Dynamics In Thymidylate Synthase Catalysis: Variants Of Conserved Dump-Binding Tyr-261
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 Strain	:	CHI2913RECA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	THYA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TS, TSASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CO3	3	Ligand/Ion	CARBONATE ION
2	CXM	2	Mod. Amino Acid	N-CARBOXYMETHIONINE
3	DTT	2	Ligand/Ion	2,3-DIHYDROXY-1,4-DITHIOBUTANE
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:50 , HIS A:51 , HOH A:317 , HOH A:517 , HOH A:655	BINDING SITE FOR RESIDUE CO3 A 803
2	AC2	SOFTWARE	CYS B:50 , HIS B:51 , HOH B:340 , HOH B:532	BINDING SITE FOR RESIDUE CO3 B 804
3	AC3	SOFTWARE	TRP A:101 , PRO A:102 , PRO A:104 , HOH A:291 , TRP B:101 , PRO B:102 , ASN B:134 , GLY B:136	BINDING SITE FOR RESIDUE CO3 B 805
4	AC4	SOFTWARE	ARG A:21 , ARG A:166 , SER A:167 , HOH A:608 , ARG B:126	BINDING SITE FOR RESIDUE PO4 A 565
5	AC5	SOFTWARE	ARG A:126 , ARG B:166 , SER B:167 , HOH B:296 , HOH B:512	BINDING SITE FOR RESIDUE PO4 B 567
6	AC6	SOFTWARE	GLU A:58 , ILE A:79 , TRP A:80 , PHE A:176 , HOH A:615 , HOH A:642 , HOH A:661	BINDING SITE FOR RESIDUE DTT A 800
7	AC7	SOFTWARE	GLU B:58 , ILE B:79 , TRP B:80 , HOH B:697	BINDING SITE FOR RESIDUE DTT B 801

(no "SS Bond" information available for 2G8X)

(no "Cis Peptide Bond" information available for 2G8X)

(no "SAP(SNP)/Variant" information available for 2G8X)

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_ECOLI	126-154	2	A:126-154 B:126-154

(no "Exon" information available for 2G8X)

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:262
 aligned with TYSY_ECOLI | P0A884 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:262
                                    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 MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPV 262
               SCOP domains d2g8xa_ A: Thymidylate synthase                                                                                                                                                                                                                                        SCOP domains
               CATH domains -2g8xA00 A:2-262 Thymidylate Synthase, chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheee.......eeeeeeeeeeee..............hhhhhhhhhhhhhh...hhhhhhh.................hhhhhhhhee.....eehhhhhhhhhhhhh.....eeee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g8x A   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLWSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPV 262
                            |       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  
                            |                                                                                                                                                                                                                                                                     
                            1-CXM

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with TYSY_ECOLI | P0A884 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:262
                                    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 MKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPV 262
               SCOP domains d2g8xb_ B: Thymidylate synthase                                                                                                                                                                                                                                        SCOP domains
               CATH domains -2g8xB00 B:2-262 Thymidylate Synthase, chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............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
                 2g8x B   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLWSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPV 262
                            |       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  
                            1-CXM

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( (-)

)

Families(

)

Protein Domains( (-)

)

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)

Escherichia coli [TaxId: 562] (64)

1a	d2g8xa_	A:
1b	d2g8xb_	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)

Escherichia coli. Organism_taxid: 562. (16)

1a	2g8xA00	A:2-262
1b	2g8xB00	B:2-262

(no "Pfam Domain" information available for 2G8X)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2g8x)

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	2g8x
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	2.1.1.45
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2g86	L. CASEI THYMIDYLATE SYNTHASE Y261F-DUMP
2g89	L. CASEI THYMIDYLATE SYNTHASE Y261A-DUMP
2g8a	L. CASEI THYMIDYLATE SYNTHASE Y261M-DUMP
2g8d	L. CASEI THYMIDYLATE SYNTHASE Y261W-DUMP
2g8m	E. COLI Y209W IN COMPLEX WITH DUMP AND CB3717
2g8o	E. COLI IN COMPLEX WITH DUMP AND CB3717

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (11, 11)

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