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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURAL AND THEORETICAL STUDIES SUGGEST DOMAIN MOVEMENT PRODUCES AN ACTIVE CONFORMATION OF THYMIDINE PHOSPHORYLASE

Authors :   M. J. Pugmire, W. J. Cook, A. Jasanoff, M. R. Walter, S. E. Ealick

Date :   24 Nov 97 (Deposition) - 13 Jan 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Glycosyltransferase, Thymidine Phosphorylase, Salvage Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Pugmire, W. J. Cook, A. Jasanoff, M. R. Walter, S. E. Ealick
Structural And Theoretical Studies Suggest Domain Movement Produces An Active Conformation Of Thymidine Phosphorylase.
J. Mol. Biol. V. 281 285 1998
PubMed-ID: 9698549 | Reference-DOI: 10.1006/JMBI.1998.1941
(for further references see the PDB file header)

Molecule 1 - THYMIDINE PHOSPHORYLASE
	Chains	:	A, B
	EC Number	:	2.4.2.4
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	MONOCLINIC CRYSTAL FORM
	Strain	:	K12

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1AZY)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	P4A	UNKNOWN	LYS A:84 , HIS A:85 , SER A:86 , SER A:95 , SER A:113 , THR A:123	PHOSPHATE BINDING SITE.
2	P4B	UNKNOWN	LYS B:84 , HIS B:85 , SER B:86 , SER B:95 , SER B:113 , THR B:123	PHOSPHATE BINDING SITE.
3	TYA	UNKNOWN	ARG A:171 , SER A:186 , LYS A:190	THYMIDINE BINDING SITE.
4	TYB	UNKNOWN	ARG B:171 , SER B:186 , LYS B:190	THYMIDINE BINDING SITE.

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

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

(no "SAP(SNP)/Variant" information available for 1AZY)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THYMID_PHOSPHORYLASE	PS00647	Thymidine and pyrimidine-nucleoside phosphorylases signature.	TYPH_ECOLI	113-128	2	A:113-128 B:113-128

(no "Exon" information available for 1AZY)

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:440
 aligned with TYPH_ECOLI | P07650 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:440
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
           TYPH_ECOLI     1 MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAAIKLADKAPESTPTVYRRISE 440
               SCOP domains d1azya1 A:1-70 Thymidine phosphorylase                                d1azya2 A:71-335 Thymidine phosphorylase                                                                                                                                                                                                                                 d1azya3 A:336-440 Thymidine phosphorylase                                                                 SCOP domains
               CATH domains 1azyA01 A:1-69,A:156-193                                             1azyA02 A:70-155,A:194-336 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2     1azyA01 A:1-69,A:156-193              1azyA02 A:70-155,A:194-336 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                              1azyA03 A:337-433  [code=3.90.1170.30, no name defined]                                          ------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh......hhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhh...eeeee.........hhhhhhh.........hhhhhhhhhhh.eeeee.......hhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeeee.......eee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhh..........hhh......eeeee......eeeee.hhhhhhhhhhh...............eee...............eeeee..hhhhhhhhhhhhhheeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1azy A   1 LFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAAIKLADKAPESTPTVYRRISE 440
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

Chain B from PDB  Type:PROTEIN  Length:440
 aligned with TYPH_ECOLI | P07650 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:440
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440
           TYPH_ECOLI     1 MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAAIKLADKAPESTPTVYRRISE 440
               SCOP domains d1azyb1 B:1-70 Thymidine phosphorylase                                d1azyb2 B:71-335 Thymidine phosphorylase                                                                                                                                                                                                                                 d1azyb3 B:336-440 Thymidine phosphorylase                                                                 SCOP domains
               CATH domains 1azyB01 B:1-69,B:156-193                                             1azyB02 B:70-155,B:194-336 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2     1azyB01 B:1-69,B:156-193              1azyB02 B:70-155,B:194-336 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                              1azyB03 B:337-433  [code=3.90.1170.30, no name defined]                                          ------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh......hhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhh...............eeeee.......hhhhhhhhhhhh...eeeee.........hhhhhhh.........hhhhhhhhhhh.eeeee.......hhhhhhhhhhh......hhhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhhhhh..eeeeeeee.......eee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhh..........hhh......eeeee......eeeee.hhhhhhhhhhh...............eee...............eeeee..hhhhhhhhhhhhhheeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1azy B   1 LFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHTGGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKLQAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALGMAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAAIKLADKAPESTPTVYRRISE 440
                                    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       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440

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 '\|'

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TYPH_ECOLI | P07650)

molecular function
	GO:0004645	phosphorylase activity	Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase.
	GO:0016154	pyrimidine-nucleoside phosphorylase activity	Catalysis of the reaction: pyrimidine nucleoside + phosphate = pyrimidine + alpha-D-ribose 1-phosphate.
	GO:0009032	thymidine phosphorylase activity	Catalysis of the reaction: thymidine + phosphate = thymine + 2-deoxy-D-ribose 1-phosphate.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
	GO:0016763	transferase activity, transferring pentosyl groups	Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0006206	pyrimidine nucleobase metabolic process	The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0006213	pyrimidine nucleoside metabolic process	The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0006220	pyrimidine nucleotide metabolic process	The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0046104	thymidine metabolic process	The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (4, 4)

SS Bonds (0, 0)

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