1QVZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE S. CEREVISIAE YDR533C PROTEIN

Authors :   M. Graille, N. Leulliot, S. Quevillon-Cheruel, H. Van Tilbeurgh

Date :   29 Aug 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Alpha/Beta Hydrolase Fold, Catalytic Triad, Heat Shock Protein, Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Graille, S. Quevillon-Cheruel, N. Leulliot, C. Z. Zhou, I. L. De La Sierra Gallay, L. Jacquamet, J. L. Ferrer, D. Liger, A. Poupon, J. Janin, H. Van Tilbeurgh
Crystal Structure Of The Ydr533C S. Cerevisiae Protein, A Class Ii Member Of The Hsp31 Family
Structure V. 12 839 2004
PubMed-ID: 15130476 | Reference-DOI: 10.1016/J.STR.2004.02.030
(for further references see the PDB file header)

Molecule 1 - YDR533C PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET9
	Expression System Strain	:	BL21(DE3)PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YDR533C
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1QVZ)

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

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

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

(no "PROSITE Motif" information available for 1QVZ)

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR533C	1	YDR533C.1	IV:1502153-1501440	714	HSP31_YEAST	1-237	237	2	A:2-237 B:2-237	236 236

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
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Chain A from PDB  Type:PROTEIN  Length:236
 aligned with HSP31_YEAST | Q04432 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
          HSP31_YEAST     2 APKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
               SCOP domains d1qvza_ A: Hypothetical protein Ydr533Cp                                                                                                                                                                                                     SCOP domains
               CATH domains 1qvzA00 A:2-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.................hhhhhhhhhhhhhhh..eeeee........hhhhhh....hhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh.eeee....hhhhhh..hhhhhhhhhhhhhh..eeeee.hhhhhhh...............ee...hhhhhhhh.hhhhhhhh...hhhhhhhhh..ee..........eeee..eeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-237 UniProt: 1-237 [INCOMPLETE]                                                                                                                                                                                           Transcript 1
                 1qvz A   2 APKKVLLALTSYNDVFYSDGmKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFmASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVcHGPAmFDGLTDKKTGRPLIEGKSITGFTDVGETImGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
                                    11        21|       31        41        51        61        71        81        91       101 |     111       121       131      |141 |     151       161       171 |     181       191       201       211       221       231      
                                               22-MSE                                                                          103-MSE                            138-CSO|                           173-MSE                                                            
                                                                                                                                                                       143-MSE

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with HSP31_YEAST | Q04432 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
          HSP31_YEAST     2 APKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
               SCOP domains d1qvzb_ B: Hypothetical protein Ydr533Cp                                                                                                                                                                                                     SCOP domains
               CATH domains 1qvzB00 B:2-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) --DJ-1_PfpI_N-1qvzB03 B:4-42             -------------------DJ-1_PfpI-1qvzB01 B:62-236                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) --DJ-1_PfpI_N-1qvzB04 B:4-42             -------------------DJ-1_PfpI-1qvzB02 B:62-236                                                                                                                                                     - Pfam domains (2)
         Sec.struct. author ...eeeee.................hhhhhhhhhhhhhhh..eeeee........hhhhhh....hhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh.eeee....hhhhhh..hhhhhhhhhhhhhh..eeeee.hhhhhhh...............ee...hhhhhhhh.hhhhhhhh...hhhhhhhhh..ee..........eeee..eeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-237 UniProt: 1-237 [INCOMPLETE]                                                                                                                                                                                           Transcript 1
                 1qvz B   2 APKKVLLALTSYNDVFYSDGmKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFmASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVcHGPAmFDGLTDKKTGRPLIEGKSITGFTDVGETImGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
                                    11        21|       31        41        51        61        71        81        91       101 |     111       121       131      |141 |     151       161       171 |     181       191       201       211       221       231      
                                               22-MSE                                                                          103-MSE                            138-CSO|                           173-MSE                                                            
                                                                                                                                                                       143-MSE

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( (-)

)

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

Fold: Flavodoxin-like (1057)

Superfamily: Class I glutamine amidotransferase-like (173)

Family: DJ-1/PfpI (54)

Protein domain: Hypothetical protein Ydr533Cp (4)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (4)

1a	d1qvza_	A:
1b	d1qvzb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.880, no name defined] (97)

Baker's yeast (Saccharomyces cerevisiae) (8)

1a	1qvzA00	A:2-237
1b	1qvzB00	B:2-237

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HSP31_YEAST | Q04432)

molecular function
	GO:0019172	glyoxalase III activity	Catalysis of the reaction: methylglyoxal + H2O = D-lactate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0031669	cellular response to nutrient levels	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 reflecting the presence, absence, or concentration of nutrients.
	GO:0034599	cellular response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0019249	lactate biosynthetic process	The chemical reactions and pathways resulting in the formation of lactate, the anion of lactic acid.
	GO:0019243	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione	The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.

Asymmetric/Biological Unit
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	HSP31_YEAST \| Q04432	:	1qvv 1qvw 4qyx

1qvv	THE SAME PROTEIN WITHOUT FOUR RESIDUES MUTATED TO METHIONINE FOR MAD PHASING
1qvw	THE SAME PROTEIN WITH FOUR RESIDUES MUTATED TO METHIONINE FOR MAD PHASING BUT NOT SELENOMET LABELLED

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