1QVV - JenaLib

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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 :   2.35

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

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, C, D
	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
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CME	4	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE

(no "Site" information available for 1QVV)

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

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

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

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

Asymmetric Unit (1, 4)

	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	4	A:4-237 B:1-237 C:3-237 D:4-237	234 237 235 234

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:234
 aligned with HSP31_YEAST | Q04432 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
          HSP31_YEAST     4 KKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
               SCOP domains d1qvva_ A: Hypothetical protein Ydr533Cp                                                                                                                                                                                                   SCOP domains
               CATH domains 1qvvA00 A:4-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee................hhhhhhhhhhhhhhhh.eeeeee.......hhhhhh.....hhhhhhhhh..hhhhhhhh...hhhhhhhhhh.eeee....hhhhhh..hhhhhhhhhhhhhh..eeee..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:4-237 UniProt: 1-237 [INCOMPLETE]                                                                                                                                                                                         Transcript 1
                 1qvv A   4 KKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVcHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    |  143       153       163       173       183       193       203       213       223       233    
                                                                                                                                                                138-CME

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

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
          HSP31_YEAST     1 MAPKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
               SCOP domains d1qvvb_ B: Hypothetical protein Ydr533Cp                                                                                                                                                                                                      SCOP domains
               CATH domains 1qvvB00 B:1-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee................hhhhhhhhhhhhhhh..eeeeee.......hhhhhh....hhhhhhhhhh..hhhhhhhhh..hhhhhhhhhh.eeee....hhhhhh..hhhhhhhhhhhhhh..eeee..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:1-237 UniProt: 1-237                                                                                                                                                                                                         Transcript 1
                 1qvv B   1 MAPKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVcHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                                                   138-CME

Chain C from PDB  Type:PROTEIN  Length:235
 aligned with HSP31_YEAST | Q04432 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:235
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
          HSP31_YEAST     3 PKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
               SCOP domains d1qvvc_ C: Hypothetical protein Ydr533Cp                                                                                                                                                                                                    SCOP domains
               CATH domains 1qvvC00 C:3-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.................hhhhhhhhhhhhhhh..eeeee........hhhhhh....hhhhhhhhhh..hhhhhhhh...hhhhhhhhhh.eeee....hhhhhh..hhhhhhhhhhhhhh..eeeee.hhhhhhh...............ee...hhhhhhhh.hhhhhhhhh..hhhhhhhhh..ee..........eeee..eeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:3-237 UniProt: 1-237 [INCOMPLETE]                                                                                                                                                                                          Transcript 1
                 1qvv C   3 PKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVcHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
                                    12        22        32        42        52        62        72        82        92       102       112       122       132     | 142       152       162       172       182       192       202       212       222       232     
                                                                                                                                                                 138-CME

Chain D from PDB  Type:PROTEIN  Length:234
 aligned with HSP31_YEAST | Q04432 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
          HSP31_YEAST     4 KKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
               SCOP domains d1qvvd_ D: Hypothetical protein Ydr533Cp                                                                                                                                                                                                   SCOP domains
               CATH domains 1qvvD00 D:4-237  [code=3.40.50.880, no name defined]                                                                                                                                                                                       CATH domains
           Pfam domains (1) DJ-1_PfpI_N-1qvvD05 D:4-42             -------------------DJ-1_PfpI-1qvvD01 D:62-236                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) DJ-1_PfpI_N-1qvvD06 D:4-42             -------------------DJ-1_PfpI-1qvvD02 D:62-236                                                                                                                                                     - Pfam domains (2)
           Pfam domains (3) DJ-1_PfpI_N-1qvvD07 D:4-42             -------------------DJ-1_PfpI-1qvvD03 D:62-236                                                                                                                                                     - Pfam domains (3)
           Pfam domains (4) DJ-1_PfpI_N-1qvvD08 D:4-42             -------------------DJ-1_PfpI-1qvvD04 D:62-236                                                                                                                                                     - Pfam domains (4)
         Sec.struct. author .eeeee.................hhhhhhhhhhhhhhh..eeeee........hhhhhh....hhhhhhhhhh..hhhhhhhh...hhhhhhhhhh.eeee....hhhhhh..hhhhhhhhhhhhhh..eeeee.hhhhhhh...............ee...hhhhhhhh.hhhhhhhh...hhhhhhhhh..ee..........eeee..eeee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: D:4-237 UniProt: 1-237 [INCOMPLETE]                                                                                                                                                                                         Transcript 1
                 1qvv D   4 KKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVcHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 237
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    |  143       153       163       173       183       193       203       213       223       233    
                                                                                                                                                                138-CME

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 Unit

Classes(

)

Folds(

)

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	d1qvva_	A:
1b	d1qvvb_	B:
1c	d1qvvc_	C:
1d	d1qvvd_	D:

Asymmetric 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	1qvvA00	A:4-237
1b	1qvvD00	D:4-237
1c	1qvvC00	C:3-237
1d	1qvvB00	B:1-237

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

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	HSP31_YEAST \| Q04432	:	1qvw 1qvz 4qyx

1qvw	THE SAME PROTEIN WITH FOUR RESIDUES MUTATED TO METHIONINE FOR MAD PHASING BUT NOT SELENOMET LABELLED
1qvz	THE SAME PROTEIN WITH FOUR RESIDUES MUTATED TO SELENOMETHIONE

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