3PIL - JenaLib

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Title :   CRYSTAL STRUCTURE OF MXR1 FROM SACCHAROMYCES CEREVISIAE IN REDUCED 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 :   2.04

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:25 , PHE A:26 , TRP A:27 , TYR A:64 , GLU A:76 , TYR A:116 , HOH A:303	BINDING SITE FOR RESIDUE ACT A 185
2	AC2	SOFTWARE	LYS A:65 , CYS B:25 , PHE B:26 , TRP B:27 , TYR B:64 , GLU B:76 , TYR B:116	BINDING SITE FOR RESIDUE ACT B 185

(no "SS Bond" information available for 3PIL)

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

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

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

(no "Exon" information available for 3PIL)

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:183
 aligned with MSRA_YEAST | P40029 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           MSRA_YEAST     1 MSSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLRE 183
               SCOP domains d3pila_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeee.hhhhhhhhhhhhhh....eeeeeee..hhhhh......hhhhhh......eeeeeeee.....hhhhhhhhhh.........ee..ee.hhh.eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee...eee.hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pil A   1 GSSLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLRE 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with MSRA_YEAST | P40029 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
           MSRA_YEAST     3 SLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLRE 183
               SCOP domains d3pilb_ B: automated matches                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------PMSR-3pilB01 B:17-179                                                                                                                                              ---- Pfam domains (1)
           Pfam domains (2) --------------PMSR-3pilB02 B:17-179                                                                                                                                              ---- Pfam domains (2)
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhhh....eeeeeee..hhhhh......hhhhhh......eeeeeeee.....hhhhhhhhhh.........ee..ee.hhh.eeeee.hhhhhhhhhhhhhhhhhhhh.....eeee...eee.hhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pil B   3 SLISKTIKYDPAKDKLITLACGCFWGTEHMYRKYLNDRIVDCKVGYANGEESKKDSPSSVSYKRVCGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLRE 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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	d3pila_	A:
1b	d3pilb_	B:

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

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-3pilB01	B:17-179
1b	PMSR-3pilB02	B:17-179

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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Biological Units
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3pim	CRYSTAL STRUCTURE OF MXR1 FROM SACCHAROMYCES CEREVISIAE IN UNUSUAL OXIDIZED FORM
3pin	CRYSTAL STRUCTURE OF MXR1 FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH TRX2

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