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Title :   CRYSTAL STRUCTURE OF YEAST ERV1 CORE

Authors :   S. Kawano, K. Terao, N. Watanabe, T. Endo

Date :   17 Jan 13 (Deposition) - 20 Mar 13 (Release) - 20 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Alpha Helix, Disulfide Bond, Redox, Tim40/Mia40, Mitochondria, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Kawano, K. Terao, N. Watanabe, T. Endo
Crystal Structure Of Yeast Erv1 Core
To Be Published
PubMed: search

Molecule 1 - MITOCHONDRIAL FAD-LINKED SULFHYDRYL OXIDASE ERV1
	Chains	:	A, B, C
	EC Number	:	1.8.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	SHUFFLE T7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 73-189
	Gene	:	ERV1, ERV1/YGR029W, YGR029W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508, S288C, W303-1A,
	Synonym	:	14 KDA REGULATORY PROTEIN, ESSENTIAL FOR RESPIRATION AND VEGETATIVE GROWTH PROTEIN 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	FAD	3	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:88 , GLY A:91 , ARG A:92 , TRP A:95 , HIS A:99 , TYR A:128 , TRP A:132 , CYS A:133 , CYS A:159 , HIS A:162 , ASN A:163 , VAL A:165 , ASN A:166 , LYS A:168 , LEU A:169 , LYS A:171 , PHE A:174 , TRP A:179 , ARG A:182 , TRP A:183 , HOH A:308 , HOH A:309 , HOH A:310 , HOH A:317 , HOH A:329 , HOH B:312 , HOH B:378 , HOH C:301	BINDING SITE FOR RESIDUE FAD A 200
2	AC2	SOFTWARE	HOH A:312 , TYR B:79 , GLU B:88 , GLY B:91 , ARG B:92 , TRP B:95 , HIS B:99 , TYR B:128 , TRP B:132 , CYS B:133 , CYS B:159 , HIS B:162 , ASN B:163 , VAL B:165 , ASN B:166 , LYS B:168 , LEU B:169 , LYS B:171 , PHE B:174 , TRP B:179 , ARG B:182 , TRP B:183 , HOH B:305 , HOH B:317 , HOH B:318 , HOH B:319 , HOH B:325 , HOH B:328 , HOH B:376 , HOH B:384	BINDING SITE FOR RESIDUE FAD B 200
3	AC3	SOFTWARE	GLU C:88 , GLY C:91 , ARG C:92 , TRP C:95 , HIS C:99 , TYR C:128 , TRP C:132 , CYS C:133 , CYS C:159 , HIS C:162 , ASN C:163 , VAL C:165 , ASN C:166 , LYS C:168 , LEU C:169 , LYS C:171 , PHE C:174 , TRP C:179 , ARG C:182 , TRP C:183 , HOH C:304 , HOH C:308 , HOH C:322 , HOH C:324 , HOH C:333 , HOH C:352 , HOH C:365	BINDING SITE FOR RESIDUE FAD C 200

Asymmetric Unit

No.	Residues
1	A:130	-	A:133
2	A:159	-	A:176
3	B:130	-	B:133
4	B:159	-	B:176
5	C:130	-	C:133
6	C:159	-	C:176

(no "Cis Peptide Bond" information available for 3W4Y)

(no "SAP(SNP)/Variant" information available for 3W4Y)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ERV1_YEAST	83-183	3	A:83-183 B:83-183 C:83-183

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ERV1_YEAST	83-183	2	A:83-183 - C:83-183

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ERV1_YEAST	83-183	2	- B:83-183 -

(no "Exon" information available for 3W4Y)

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:113
 aligned with ERV1_YEAST | P27882 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:113
                                    85        95       105       115       125       135       145       155       165       175       185   
           ERV1_YEAST    76 SRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
               SCOP domains d3w4ya_ A: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------ERV_ALR  PDB: A:83-183 UniProt: 83-183                                                               ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3w4y A  76 SRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
                                    85        95       105       115       125       135       145       155       165       175       185

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with ERV1_YEAST | P27882 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:118
                                    80        90       100       110       120       130       140       150       160       170       180        
           ERV1_YEAST    71 ELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
               SCOP domains d3w4yb_ B: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------ERV_ALR  PDB: B:83-183 UniProt: 83-183                                                               ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3w4y B  71 SHMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
                                    80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with ERV1_YEAST | P27882 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:128
                                    70        80        90       100       110       120       130       140       150       160       170       180        
           ERV1_YEAST    61 GTGALTGEASELMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
               SCOP domains d3         w4yc_ C: automated matches                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---------..............hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------ERV_ALR  PDB: C:83-183 UniProt: 83-183                                                               ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w4y C  70 GS---------HMPGSRTYRKVDPPDVEQLGRSSWTLLHSVAASYPAQPTDQQKGEMKQFLNIFSHIYPCNWCAKDFEKYIRENAPQVESREELGRWMCEAHNKVNKKLRKPKFDCNFWEKRWKDGWD 188
                             |       - |      80        90       100       110       120       130       140       150       160       170       180        
                            71        72

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: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: FAD-dependent thiol oxidase (15)

Family: automated matches (5)

Protein domain: automated matches (5)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292] (3)

1a	d3w4ya_	A:
1b	d3w4yb_	B:
1c	d3w4yc_	C:

(no "CATH Domain" information available for 3W4Y)

(no "Pfam Domain" information available for 3W4Y)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ERV1_YEAST | P27882)

molecular function
	GO:0016971	flavin-linked sulfhydryl oxidase activity	Catalysis of the formation of disulfide bridges.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016972	thiol oxidase activity	Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O.
biological process
	GO:0006879	cellular iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
	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:0045041	protein import into mitochondrial intermembrane space	The import of proteins into the space between the inner and outer mitochondrial membranes.
	GO:0006626	protein targeting to mitochondrion	The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
cellular component
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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SS Bonds (6, 6)

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