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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF YEAST FREE METHIONINE-R-SULFOXIDE REDUCTASE YKG9 IN COMPLEX WITH THE SUBSTRATE

Authors :   X. -X. Ma, P. -C. Guo, Y. Chen, C. -Z. Zhou

Date :   13 Nov 09 (Deposition) - 17 Nov 10 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

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

Keywords :   Saccharomyces Cerevisiae, Methionine-R-Sulfoxide Reductase, Substrate Binding, Catalytic Mechanism, Product Dissociation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. -X. Ma, P. -C. Guo, Y. Chen, C. -Z. Zhou
Crystal Structure Of Yeast Free Methionine-R-Sulfoxide Reductase Ykg9 In Complex With The Substrate
To Be Published
PubMed: search

Molecule 1 - UPF0067 GAF DOMAIN-CONTAINING PROTEIN YKL069W
	Chains	:	A, B
	EC Number	:	1.8.4.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YKL069W
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	S288C
	Synonym	:	YKG9

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SME	2	Mod. Residue	METHIONINE SULFOXIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:70 , ILE A:94 , GLY A:99 , VAL A:100 , CYS A:101 , HIS A:122 , ILE A:123 , CYS A:125 , GLU A:132 , ASP A:149 , ASP A:151 , HOH A:182 , HOH A:201	BINDING SITE FOR RESIDUE SME A 181
2	AC2	SOFTWARE	TYR B:70 , ILE B:94 , GLY B:99 , VAL B:100 , CYS B:101 , HIS B:122 , ILE B:123 , CYS B:125 , GLU B:132 , ASP B:149 , ASP B:151 , HOH B:206 , HOH B:235	BINDING SITE FOR RESIDUE SME B 181

Asymmetric/Biological Unit

No.	Residues
1	A:91	-	A:125
2	B:91	-	B:125

(no "Cis Peptide Bond" information available for 3KO6)

(no "SAP(SNP)/Variant" information available for 3KO6)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UPF0067	PS01320	Uncharacterized protein family UPF0067 signature.	FRMSR_YEAST	115-132	2	A:115-132 B:115-132

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	YKL069W	1	YKL069W.1	XI:306929-307471	543	FRMSR_YEAST	1-180	180	2	A:4-179 B:4-179	176 176

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:176
 aligned with FRMSR_YEAST | P36088 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
          FRMSR_YEAST     4 STGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
               SCOP domains d3ko6a_ A: Hypothetical protein ykl069wp                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeeee.....eee..hhhhhhhhhhh..eee.hhhhh...........eeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------UPF0067           ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-179 UniProt: 1-180 [INCOMPLETE]                                                                                                                               Transcript 1
                 3ko6 A   4 STGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with FRMSR_YEAST | P36088 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
          FRMSR_YEAST     4 STGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
               SCOP domains d3ko6b_ B: Hypothetical protein ykl069wp                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------GAF_2-3ko6B01 B:18-174                                                                                                                                       ----- Pfam domains (1)
           Pfam domains (2) --------------GAF_2-3ko6B02 B:18-174                                                                                                                                       ----- Pfam domains (2)
         Sec.struct. author ....hhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...eeeeeeeee......eeeeeeeee.....eee..hhhhhhhhhhh..eee.hhhhh...........eeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------UPF0067           ----------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:4-179 UniProt: 1-180 [INCOMPLETE]                                                                                                                               Transcript 1
                 3ko6 B   4 STGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVF 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Profilin-like (304)

Superfamily: GAF domain-like (54)

Family: GAF domain (24)

Protein domain: Hypothetical protein ykl069wp (2)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d3ko6a_	A:
1b	d3ko6b_	B:

(no "CATH Domain" information available for 3KO6)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GAF (44)

Family: GAF_2 (2)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (1)

1a	GAF_2-3ko6B01	B:18-174
1b	GAF_2-3ko6B02	B:18-174

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FRMSR_YEAST | P36088)

molecular function
	GO:0033745	L-methionine-(R)-S-oxide reductase activity	Catalysis of the reaction: L-methionine + thioredoxin disulfide + H2O = L-methionine (R)-S-oxide + thioredoxin.
	GO:0070191	methionine-R-sulfoxide reductase activity	Catalysis of the reaction: L-methionine R-oxide + thioredoxin = L-methionine + thioredoxin disulfide; can act on free oxidized methionine with specificity for the R enantiomer; does not act on oxidized methionine in peptide linkage. Thioredoxin disulfide is the oxidized form of thioredoxin.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	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:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 3KO6)

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (1, 2)

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