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Title :   CRYSTAL STRUCTURE OF MXR1 FROM SACCHAROMYCES CEREVISIAE IN UNUSUAL OXIDIZED FORM

Authors :   X. X. Ma, P. C. Guo, W. W. Shi, M. Luo, X. F. Tan, Y. Chen, C. Z. Zhou

Date :   07 Nov 10 (Deposition) - 23 Feb 11 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Methionine-S-Sulfoxide Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. X. Ma, P. C. Guo, W. W. Shi, M. Luo, X. F. Tan, Y. Chen, C. Z. Zhou
Structural Plasticity Of The Thioredoxin Recognition Site O Yeast Methionine S-Sulfoxide Reductase Mxr1
J. Biol. Chem. V. 286 13430 2011
PubMed-ID: 21345799 | Reference-DOI: 10.1074/JBC.M110.205161

Molecule 1 - PEPTIDE METHIONINE SULFOXIDE REDUCTASE
	Chains	:	A, B, C
	EC Number	:	1.8.4.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MXR1
	Organism Common	:	YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	MXR1, PEPTIDE-METHIONINE (S)-S-OXIDE REDUCTASE, PEPTIDE MET(O) REDUCTASE, PROTEIN-METHIONINE-S-OXIDE REDUCTASE

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3PIM)

(no "Site" information available for 3PIM)

Asymmetric Unit

No.	Residues
1	A:25	-	B:25
2	A:68	-	A:176
3	B:68	-	B:176

Asymmetric Unit

No.	Residues
1	Asn A:106	-	Ser A:107
2	Glu C:53	-	Ser C:54
3	Cys C:68	-	Gly C:69

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

(no "PROSITE Motif" information available for 3PIM)

(no "Exon" information available for 3PIM)

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:173
 aligned with MSRA_YEAST | P40029 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:187
                               1                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       
           MSRA_YEAST     - ---MSSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM 184
               SCOP domains d3pima_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...........eeeeee..hhhhhhhhhhhhhhhhh.eeeeeeeee..---------............eeeeeeee.....hhhhhhhhhh..........-----hhhhh.eeee.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeehhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pim A  -2 HHHGSSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEE---------SYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNS-----GTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM 184
                                     7        17        27        37        47     |   -     |  67        77        87        97       107     | 117       127       137       147       157       167       177       
                                                                                  53        63                                         107   113

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with MSRA_YEAST | P40029 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:187
                               1                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       
           MSRA_YEAST     - ---MSSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM 184
               SCOP domains d3pimb_ B: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...........eeeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeee...---------...........eeeeeeee.....hhhhhhhhhh.....hhhhh...-.hhhh.eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeehhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pim B  -2 HHHGSSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEES---------YKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGP-KGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM 184
                                     7        17        27        37        47      |  -      | 67        77        87        97       107  | |  117       127       137       147       157       167       177       
                                                                                   54        64                                           110 |                                                                        
                                                                                                                                            112

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with MSRA_YEAST | P40029 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
           MSRA_YEAST     2 SSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM 184
               SCOP domains d3pimc_ C: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------PMSR-3pimC01 C:17-179                                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) ---------------PMSR-3pimC02 C:17-179                                                                                                                                              ----- Pfam domains (2)
           Pfam domains (3) ---------------PMSR-3pimC03 C:17-179                                                                                                                                              ----- Pfam domains (3)
         Sec.struct. author ...............eeeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeee...------------........eeeeeeee.....hhhhhhhhhh........--------....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeehhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pim C   2 SSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEES------------VCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTS--------TQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM 184
                                    11        21        31        41        51  |      -     |  71        81        91       101   |     -  |    121       131       141       151       161       171       181   
                                                                               54           67                                   105      114

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) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Peptide methionine sulfoxide reductase (11)

Family: automated matches (3)

Protein domain: automated matches (3)

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

1a	d3pima_	A:
1b	d3pimb_	B:
1c	d3pimc_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PMSR] (4)

Family: PMSR (4)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

1a	PMSR-3pimC01	C:17-179
1b	PMSR-3pimC02	C:17-179
1c	PMSR-3pimC03	C:17-179

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (MSRA_YEAST | P40029)

molecular function
	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.
	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	GO:0008113	peptide-methionine (S)-S-oxide reductase activity	Catalysis of the reactions: peptide-L-methionine + thioredoxin disulfide + H2O = peptide-L-methionine (S)-S-oxide + thioredoxin, and L-methionine + thioredoxin disulfide + H2O = L-methionine (S)-S-oxide + thioredoxin. Can act on oxidized methionine in peptide linkage with specificity for the S enantiomer. Thioredoxin disulfide is the oxidized form of thioredoxin.
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.
	GO:0030091	protein repair	The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asn A:106 - Ser A:107	[ RasMol ]
		Cys C:68 - Gly C:69	[ RasMol ]
		Glu C:53 - Ser C:54	[ RasMol ]

Biological Units
	Complete Structure
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	MSRA_YEAST \| P40029	:	3pil 3pin

3pil	CRYSTAL STRUCTURE OF MXR1 FROM SACCHAROMYCES CEREVISIAE IN REDUCED FORM
3pin	CRYSTAL STRUCTURE OF MXR1 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH TRX2

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