1TXZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF YEAST YMX7, AN ADP-RIBOSE-1''-MONOPHOSPHATASE, COMPLEXED WITH ADP-RIBOSE

Authors :   D. Kumaran, S. Swaminathan, S. K. Burley, New York Sgx Research Cen Structural Genomics (Nysgxrc)

Date :   06 Jul 04 (Deposition) - 30 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Structural Genomics, Dimer, Two Domain Organization, Adp-Ribose Complex, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kumaran, S. Eswaramoorthy, F. W. Studier, S. Swaminathan
Structure And Mechanism Of Adp-Ribose-1''-Monophosphatase (Appr-1''-Pase), A Ubiquitous Cellular Processing Enzyme.
Protein Sci. V. 14 719 2005
PubMed-ID: 15722447 | Reference-DOI: 10.1110/PS.041132005

Molecule 1 - HYPOTHETICAL 32.1 KDA PROTEIN IN ADH3-RCA1 INTERGENIC REGION
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YMR087W, YM9582.12
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	YMX7

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A
Biological Unit 2 (1x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	APR	2	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	APR	1	Ligand/Ion	ADENOSINE-5-DIPHOSPHORIBOSE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION
4	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:113 , HIS A:115 , SER A:119 , ASN A:176 , HIS A:180 , HOH A:293 , HOH A:303 , HOH A:312 , HOH A:320	BINDING SITE FOR RESIDUE SO4 A 287
2	AC2	SOFTWARE	GLY A:52 , HIS A:53 , SER A:56 , ASN A:95	BINDING SITE FOR RESIDUE SO4 A 288
3	AC3	SOFTWARE	PRO A:78 , GLY A:87 , PHE A:89 , ASP A:90 , APR A:285	BINDING SITE FOR RESIDUE NA A 289
4	AC4	SOFTWARE	ASP A:23 , THR A:24 , GLY A:52 , HIS A:53 , LEU A:54 , GLN A:55 , PRO A:78 , GLY A:79 , ASN A:80 , TYR A:84 , GLY A:87 , GLY A:88 , PHE A:89 , ASP A:90 , ALA A:92 , THR A:148 , VAL A:149 , GLY A:192 , CYS A:194 , THR A:195 , GLY A:196 , TYR A:197 , ALA A:198 , EDO A:286 , NA A:289 , HOH A:300 , HOH A:376	BINDING SITE FOR RESIDUE APR A 285
5	AC5	SOFTWARE	GLY A:86 , GLY A:87 , PRO A:152 , PHE A:239 , APR A:285 , HOH A:376	BINDING SITE FOR RESIDUE EDO A 286

Asymmetric Unit

No.	Residues
1	A:128	-	A:136

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MACRO	PS51154	Macro domain profile.	YMX7_YEAST	34-230	1	A:34-230

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MACRO	PS51154	Macro domain profile.	YMX7_YEAST	34-230	2	A:34-230

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MACRO	PS51154	Macro domain profile.	YMX7_YEAST	34-230	1	A:34-230

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YMR087W	1	YMR087W.1	XIII:442526-443380	855	YMX7_YEAST	1-284	284	1	A:16-279 (gaps)	264

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
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Chain A from PDB  Type:PROTEIN  Length:249
 aligned with YMX7_YEAST | Q04299 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:264
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275    
           YMX7_YEAST    16 KMRIILCDTNEVVTNLWQESIPHAYIQNDKYLCIHHGHLQSLMDSMRKGDAIHHGHSYAIVSPGNSYGYLGGGFDKALYNYFGGKPFETWFRNQLGGRYHTVGSATVVDLQRCLEEKTIECRDGIRYIIHVPTVVAPSAPIFNPQNPLKTGFEPVFNAMWNALMHSPKDIDGLIIPGLCTGYAGVPPIISCKSMAFALRLYMAGDHISKELKNVLIMYYLQYPFEPFFPESCKIECQKLGIDIEMLKSFNVEKDAIELLIPRRI 279
               SCOP domains d1txza_ A: Hypothetica       l protein Ymr087W                                                                                                                                                                                                                           SCOP domains
               CATH domains 1txzA00 A:16-279 Leuci       ne Aminopeptidase, sub    unit E, domain 1                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhh.-------..eeeee.hhhhhhhhh.....----..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh..........eeee.hhhhh----.....eeeeeeeeee................hhhhhhhhhhhhhhh......eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhh......hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------MACRO  PDB: A:34-230 UniProt: 34-230                                                                                                                                                                 ------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:16-279 (gaps) UniProt: 1-284 [INCOMPLETE]                                                                                                                                                                                                               Transcript 1
                 1txz A  16 KMRIILCDTNEVVTNLWQESIP-------KYLCIHHGHLQSLMDSMRKGDA----HSYAIVSPGNSYGYLGGGFDKALYNYFGGKPFETWFRNQLGGRYHTVGSATVVDLQRCLE----ECRDGIRYIIHVPTVVAPSAPIFNPQNPLKTGFEPVFNAMWNALMHSPKDIDGLIIPGLCTGYAGVPPIISCKSMAFALRLYMAGDHISKELKNVLIMYYLQYPFEPFFPESCKIECQKLGIDIEMLKSFNVEKDAIELLIPRRI 279
                                    25        35 |      45        55        65|    |  75        85        95       105       115       125    |  135       145       155       165       175       185       195       205       215       225       235       245       255       265       275    
                                                37      45                   66   71                                                        130  135

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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

Fold: Macro domain-like (42)

Superfamily: Macro domain-like (42)

Family: Macro domain (20)

Protein domain: Hypothetical protein Ymr087W (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

d1txza_

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Leucine Aminopeptidase, subunit E; domain 1 (21)

Homologous Superfamily: Leucine Aminopeptidase, subunit E, domain 1 (21)

Baker's yeast (Saccharomyces cerevisiae) (3)

1txzA00

A:16-279

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

Asymmetric Unit(hide GO term definitions)

Chain A (YMX7_YEAST | Q04299)

molecular function
	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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006388	tRNA splicing, via endonucleolytic cleavage and ligation	Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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	YMX7_YEAST \| Q04299	:	1njr 1ty8

1njr	CRYSTAL STRUCTURE OF YEAST HYPOTHETICAL PROTEIN YMX7 RELATED ID: NYSGXRC-P089 RELATED DB: TARGETDB

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