2G80 - JenaLib

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Title :   CRYSTAL STRUCTURE OF UTR4 PROTEIN (UNKNOWN TRANSCRIPT 4 PROTEIN) (YEL038W) FROM SACCHAROMYCES CEREVISIAE AT 2.28 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   01 Mar 06 (Deposition) - 28 Mar 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Yel038W, Utr4 Protein (Unknown Transcript 4 Protein), Structural Genomics, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Jcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Utr4 Protein (Unknown Transcript 4 Protein) (Yel038W) From Saccharomyces Cerevisiae At 2. 28 A Resolution
To Be Published
PubMed: search

Molecule 1 - PROTEIN UTR4
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	UTR4
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	UNKNOWN TRANSCRIPT 4 PROTEIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MG	6	Ligand/Ion	MAGNESIUM ION
3	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PE4	1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:25 , GLU A:27 , ASP A:200 , HOH A:509 , HOH A:517 , HOH A:593	BINDING SITE FOR RESIDUE MG A 500
2	AC2	SOFTWARE	ASP B:25 , GLU B:27 , ASP B:200 , HOH B:515 , HOH B:548 , HOH B:559	BINDING SITE FOR RESIDUE MG B 500
3	AC3	SOFTWARE	ASP C:25 , GLU C:27 , ASP C:200 , HOH C:510 , HOH C:511 , HOH C:548	BINDING SITE FOR RESIDUE MG C 500
4	AC4	SOFTWARE	ASP D:25 , GLU D:27 , ASP D:200 , HOH D:562 , HOH D:563 , HOH D:564	BINDING SITE FOR RESIDUE MG D 500
5	AC5	SOFTWARE	HIS A:79 , ASP A:90 , HOH A:575 , HOH A:601 , ASP C:90 , HOH C:572 , HOH C:573	BINDING SITE FOR RESIDUE MG C 501
6	AC6	SOFTWARE	ASP D:90 , HOH D:541 , HOH D:565 , HOH D:566	BINDING SITE FOR RESIDUE MG D 501
7	AC7	SOFTWARE	PRO A:113 , VAL A:114 , TYR A:115 , GLN A:147 , GLU B:38	BINDING SITE FOR RESIDUE PE4 A 501
8	AC8	SOFTWARE	GLU C:38 , PRO D:113 , GLN D:147 , PRO D:149 , HOH D:504 , HOH D:533	BINDING SITE FOR RESIDUE GOL D 502
9	AC9	SOFTWARE	ALA C:78	BINDING SITE FOR RESIDUE GOL C 502

(no "SS Bond" information available for 2G80)

(no "Cis Peptide Bond" information available for 2G80)

(no "SAP(SNP)/Variant" information available for 2G80)

(no "PROSITE Motif" information available for 2G80)

Asymmetric Unit (1, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YEL038W	1	YEL038W.1	V:80462-81145	684	ENOPH_YEAST	1-227	227	4	A:17-241 B:18-241 C:18-241 D:18-241 (gaps)	225 224 224 224

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:225
 aligned with ENOPH_YEAST | P32626 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:225
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
          ENOPH_YEAST     3 DNYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 227
               SCOP domains d2g80a1 A:17-241 Protein UTR4                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeee...hhhhhhhhhhh.............hhhhh.eeehhhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee...............ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:17-241 UniProt: 1-227 [INCOMPLETE]                                                                                                                                                                               Transcript 1
                 2g80 A  17 DNYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 241
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with ENOPH_YEAST | P32626 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
          ENOPH_YEAST     4 NYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 227
               SCOP domains d2g80b_ B: Protein UTR4                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..eeee...hhhhhhhhhhh.............hhhhh.eeehhhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee...............ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:18-241 UniProt: 1-227 [INCOMPLETE]                                                                                                                                                                              Transcript 1
                 2g80 B  18 NYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 241
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

Chain C from PDB  Type:PROTEIN  Length:224
 aligned with ENOPH_YEAST | P32626 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
          ENOPH_YEAST     4 NYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 227
               SCOP domains d2g80c_ C: Protein UTR4                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhh....eeee...hhhhhhhhhhh.............hhhhh.eeehhhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee...............ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:18-241 UniProt: 1-227 [INCOMPLETE]                                                                                                                                                                              Transcript 1
                 2g80 C  18 NYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 241
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

Chain D from PDB  Type:PROTEIN  Length:221
 aligned with ENOPH_YEAST | P32626 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
          ENOPH_YEAST     4 NYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPVPDGQKYQVYKNFETL 227
               SCOP domains d2g80d_ D: Protein UTR4                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.eeeee...hhhhhhhhh...............hhhhh.eeehhhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhh...eeeee........---....ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:18-241 (gaps) UniProt: 1-227 [INCOMPLETE]                                                                                                                                                                       Transcript 1
                 2g80 D  18 NYSTYLLDIEGTVCPISFVKETLFPYFTNKVPQLVQQDTRDSPVSNILSQFHIDNKEQLQAHILELVAKDVKDPILKQLQGYVWAHGYESGQIKAPVYADAIDFIKRKKRVFIYSSGSVKAQKLLFGYVQDPNAPAHDSLDLNSYIDGYFDINTSGKKTETQSYANILRDIGAKASEVLFLSDNPLELDAAAGVGIATGLASRPGNAPV---QKYQVYKNFETL 241
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217        |-  |    237    
                                                                                                                                                                                                                                          226 230

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: Enolase-phosphatase E1 (3)

Protein domain: Protein UTR4 (1)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (1)

1a	d2g80a1	A:17-241
1b	d2g80b_	B:
1c	d2g80c_	C:
1d	d2g80d_	D:

(no "CATH Domain" information available for 2G80)

(no "Pfam Domain" information available for 2G80)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ENOPH_YEAST | P32626)

molecular function
	GO:0043715	2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity	Catalysis of the reaction: 2,3-diketo-5-methylthiopentyl-1-phosphate = H+ + 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate. 2,3-diketo-5-methylthiopentyl-1-phosphate is also known as DK-MTP-1-P, and 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate as HK-MTPenyl-1-P.
	GO:0043716	2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase activity	Catalysis of the reaction: 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate. 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate is also known as HK-MTPenyl-P, and 1,2-dihydroxy-3-keto-5-methylthiopentene as DHK-MTPene.
	GO:0043874	acireductone synthase activity	Catalysis of the reactions: 5-(methylthio)-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate; (1a) 5-(methylthio)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate; (1b) 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0019284	L-methionine salvage from S-adenosylmethionine	The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
	GO:0019509	L-methionine salvage from methylthioadenosine	The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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Description

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Ligands, Modified Residues, Ions (3, 9)

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Exons (1, 4)

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