1VRS - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DISULFIDE-LINKED COMPLEX BETWEEN THE N-TERMINAL AND C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD

Authors :   A. Rozhkova, C. U. Stirnimann, P. Frei, U. Grauschopf, R. Brunisholz, M. G. Gruetter, G. Capitani, R. Glockshuber

Date :   17 Jun 05 (Deposition) - 12 Jul 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,E  (1x)
Biol. Unit 3: C,F  (1x)

Keywords :   Dsbd, Immunoglobulin-Like, Thioredoxin-Like, Disulfide-Linked, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Rozhkova, C. U. Stirnimann, P. Frei, U. Grauschopf, R. Brunisholz, M. G. Gruetter, G. Capitani, R. Glockshuber
Structural Basis And Kinetics Of Inter- And Intramolecular Disulfide Exchange In The Redox Catalyst Dsbd
Embo J. V. 23 1709 2004
PubMed-ID: 15057279 | Reference-DOI: 10.1038/SJ.EMBOJ.7600178

Molecule 1 - THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD
	Chains	:	A, B, C
	EC Number	:	1.8.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDSBA3
	Expression System Strain	:	BL21ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL DOMAIN, RESIDUES 1-143
	Gene	:	DSBD, DIPZ, CYCZ, CUTA2, B4136
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI STR. K12 SUBSTR.
	Organism Taxid	:	316407
	Strain	:	W3110
	Synonym	:	PROTEIN-DISULFIDE REDUCTASE, C-TYPE CYTOCHROME BIOGENESIS PROTEIN CYCZ, INNER MEMBRANE COPPER TOLERANCE PROTEIN

Molecule 2 - THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD
	Chains	:	D, E, F
	EC Number	:	1.8.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDSBA3
	Expression System Strain	:	BL21ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, RESIDUES 438-565
	Gene	:	DSBD, DIPZ, CYCZ, CUTA2, B4136
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI STR. K12 SUBSTR.
	Organism Taxid	:	316407
	Strain	:	W3110
	Synonym	:	PROTEIN-DISULFIDE REDUCTASE, C-TYPE CYTOCHROME BIOGENESIS PROTEIN CYCZ, INNER MEMBRANE COPPER TOLERANCE PROTEIN

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B			E
Biological Unit 3 (1x)	:			C			F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1VRS)

(no "Site" information available for 1VRS)

Asymmetric Unit

No.	Residues
1	A:109	-	D:461
2	B:109	-	E:461
3	C:109	-	F:461

Asymmetric Unit

No.	Residues
1	Leu D:510	-	Pro D:511
2	Leu E:510	-	Pro E:511
3	Leu F:510	-	Pro F:511

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBD_ECOLI	472-490	3	D:453-471 E:453-471 F:453-471

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBD_ECOLI	472-490	1	D:453-471 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBD_ECOLI	472-490	1	- E:453-471 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBD_ECOLI	472-490	1	- - F:453-471

(no "Exon" information available for 1VRS)

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:121
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:125
                                    29        39        49        59        69        79        89        99       109       119       129       139     
           DSBD_ECOLI    20 GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGCADAGFCYPPETKTVPLSEVVAN 144
               SCOP domains d1vrs    a_ A: Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)                                       SCOP domains
               CATH domains 1vrsA    00 A:1-125  [code=2.60.40.1250, no name defined]                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....----...hhhhheeeeeeee..eeeeeeee...eeee.hhheeeeeeeee........eeeee...eeeeee..eeeeeeeeeeeeeeeeeeeee.eee...ee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrs A   1 GLFDA----QFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSEVVAN 125
                                |   10        20        30        40        50        60        70        80        90       100       110       120     
                                5   10

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:125
                                    29        39        49        59        69        79        89        99       109       119       129       139     
           DSBD_ECOLI    20 GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGCADAGFCYPPETKTVPLSEVVAN 144
               SCOP domains d1vrsb_ B: Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)                                           SCOP domains
               CATH domains 1vrsB00 B:1-125  [code=2.60.40.1250, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhheeeeeeee..eeeeeeee...eeee.hhheeeeeeeee........eeee.....eeeee..eeeeeeeeeeeeeeeeeeeee.eee...ee...eeeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrs B   1 GLFDAPGRSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSEVVAN 125
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:113
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:113
                                    37        47        57        67        77        87        97       107       117       127       137   
           DSBD_ECOLI    28 SQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGCADAGFCYPPETKTVPLSE 140
               SCOP domains d1vrsc_ C: Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)                               SCOP domains
               CATH domains 1vrsC00 C:9-121  [code=2.60.40.1250, no name defined]                                                             CATH domains
           Pfam domains (1) DsbC-1vrsC01 C:9-121                                                                                              Pfam domains (1)
           Pfam domains (2) DsbC-1vrsC02 C:9-121                                                                                              Pfam domains (2)
           Pfam domains (3) DsbC-1vrsC03 C:9-121                                                                                              Pfam domains (3)
         Sec.struct. author ....hhhhheeeeeeee..eeeeeeee...eeee.hhheeeeeeeee........eeeee...eeeeee..eeeeeeeeeeeeeeeeeeeee.eee...ee...eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1vrs C   9 SQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSE 121
                                    18        28        38        48        58        68        78        88        98       108       118

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:118
                                   456       466       476       486       496       506       516       526       536       546       556        
           DSBD_ECOLI   447 HLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVACKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQ 564
               SCOP domains d1vrsd_ D: Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma)                                    SCOP domains
               CATH domains 1vrsD00 D:428-545 Glutaredoxin                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhhhhhhhhh....eeeeee...hhhhhhhhhhh..hhhhhhhh...eeeeee....hhhhhhhhhhhh.....eeeee......hhhhhee...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrs D 428 HLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVASKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQ 545
                                   437       447       457       467       477       487       497       507       517       527       537

Chain E from PDB  Type:PROTEIN  Length:118
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:118
                                   454       464       474       484       494       504       514       524       534       544       554        
           DSBD_ECOLI   445 QTHLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVACKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRD 562
               SCOP domains d1vrse_ E: Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma)                                    SCOP domains
               CATH domains 1vrsE00 E:426-543 Glutaredoxin                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..hhhhhhhh...eeeeee....hhhhhhhhhhhh.....eeeee......hhhhhee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------THIOREDOXIN_1      ------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrs E 426 QTHLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVASKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRD 543
                                   435       445       455       465       475       485       495       505       515       525       535

Chain F from PDB  Type:PROTEIN  Length:118
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:118
                                   456       466       476       486       496       506       516       526       536       546       556        
           DSBD_ECOLI   447 HLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVACKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQ 564
               SCOP domains d1vrsf_ F: Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma)                                    SCOP domains
               CATH domains 1vrsF00 F:428-545 Glutaredoxin                                                                                         CATH domains
           Pfam domains (1) -------Thioredoxin_7-1vrsF01 F:435-518                                                     --------------------------- Pfam domains (1)
           Pfam domains (2) -------Thioredoxin_7-1vrsF02 F:435-518                                                     --------------------------- Pfam domains (2)
           Pfam domains (3) -------Thioredoxin_7-1vrsF03 F:435-518                                                     --------------------------- Pfam domains (3)
         Sec.struct. author ....ee..hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..hhhhhhhh...eeeeee....hhhhhhhhhhh......eeeee......hhhhhee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------THIOREDOXIN_1      -------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1vrs F 428 HLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVASKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQ 545
                                   437       447       457       467       477       487       497       507       517       527       537

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

K12 substr (Escherichia coli str) (1)

1a	1vrsD00	D:428-545
1b	1vrsE00	E:426-543
1c	1vrsF00	F:428-545

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1250, no name defined] (5)

K12 substr (Escherichia coli str) (1)

2a	1vrsA00	A:1-125
2b	1vrsB00	B:1-125
2c	1vrsC00	C:9-121

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Thioredoxin_7 (4)

Escherichia coli (strain K12) (1)

1a	Thioredoxin_7-1vrsF01	F:435-518
1b	Thioredoxin_7-1vrsF02	F:435-518
1c	Thioredoxin_7-1vrsF03	F:435-518

Clan: no clan defined [family: DsbC] (6)

Family: DsbC (6)

Escherichia coli (strain K12) (5)

2a	DsbC-1vrsC01	C:9-121
2b	DsbC-1vrsC02	C:9-121
2c	DsbC-1vrsC03	C:9-121

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (DSBD_ECOLI | P36655)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
	GO:0047134	protein-disulfide reductase activity	Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
	GO:0022865	transmembrane electron transfer carrier	Enables electron flow across a biological membrane, from donors localized on one side of the membrane to acceptors localized on the other side. These systems contribute to or subtract from the membrane potential, depending on the direction of electron flow. They are therefore important to cellular energetics.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0071502	cellular response to temperature stimulus	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 temperature stimulus.
	GO:0017004	cytochrome complex assembly	The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
	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:0042493	response to drug	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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1vrs)

	Sites
(no "Sites" information available for 1vrs)

	Cis Peptide Bonds
		Leu D:510 - Pro D:511	[ RasMol ]
		Leu E:510 - Pro E:511	[ RasMol ]
		Leu F:510 - Pro F:511	[ RasMol ]

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Access by PDB/NDB ID
	1vrs
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	DSBD_ECOLI \| P36655
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	1.8.1.8
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	DSBD_ECOLI \| P36655	:	1jpe 1jzd 1l6p 1z5y 2fwe 2fwf 2fwg 2fwh 3pfu 4ip1 4ip6

(no "Related Entries Specified in the PDB File" available for 1VRS)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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