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

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

Date :   21 Mar 05 (Deposition) - 19 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym./Biol. Unit : D,E

Keywords :   Dsbd, N-Terminal Domain, Immunoglobulin-Like, Ccmg, Thioredoxin-Like, Disulfide-Linked, Oxidoreductase/Biosynthetic Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. U. Stirnimann, A. Rozhkova, U. Grauschopf, M. G. Gruetter, R. Glockshuber, G. Capitani
Structural Basis And Kinetics Of Dsbd-Dependent Cytochrome C Maturation
Structure V. 13 985 2005
PubMed-ID: 16004871 | Reference-DOI: 10.1016/J.STR.2005.04.014
(for further references see the PDB file header)

Molecule 1 - THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD
	Chains	:	D
	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
	Organism Taxid	:	562
	Synonym	:	DISULFIDE INTERCHANGE PROTEIN DSBD, PROTEIN- DISULFIDE REDUCTASE, DISULFIDE REDUCTASE, C-TYPE CYTOCHROME BIOGENESIS PROTEIN CYCZ, INNER MEMBRANE COPPER TOLERANCE PROTEIN

Molecule 2
	Chains	:	E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEC86
	Expression System Strain	:	BL21TUNER(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SOLUBLE DOMAIN, RESIDUES 43-185
	Gene	:	DSBE, CCMG
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	CYTOCHROME C BIOGENESIS PROTEIN CCMG

		1	2
Asymmetric/Biological Unit	:	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN D:26 , HOH D:2021	BINDING SITE FOR RESIDUE CL E 1001
2	AC2	SOFTWARE	HIS D:52 , SER D:91 , HOH D:2167	BINDING SITE FOR RESIDUE CL D 1002
3	AC3	SOFTWARE	PRO E:56	BINDING SITE FOR RESIDUE CL E 1003
4	AC4	SOFTWARE	TYR D:42 , LYS D:44 , GLN D:45 , GLN D:101 , HOH D:2096 , TRP E:79	BINDING SITE FOR RESIDUE EDO D 2001
5	AC5	SOFTWARE	ALA D:14 , PHE D:18 , GLN D:101 , GLY D:102 , TYR D:110 , PRO D:111 , GLU D:113 , HOH D:2046	BINDING SITE FOR RESIDUE EDO D 2002
6	AC6	SOFTWARE	EDO D:2004 , HOH D:2142 , HOH D:2144 , HOH D:2168 , HOH D:2169 , LEU E:116 , LYS E:117 , GLY E:120 , ASN E:121	BINDING SITE FOR RESIDUE EDO D 2003
7	AC7	SOFTWARE	EDO D:2003 , HOH D:2102 , LEU E:119 , GLY E:120	BINDING SITE FOR RESIDUE EDO D 2004

Asymmetric/Biological Unit

No.	Residues
1	D:109	-	E:80

Asymmetric/Biological Unit

No.	Residues
1	Ala E:143	-	Pro E:144

(no "SAP(SNP)/Variant" information available for 1Z5Y)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBE_ECOLI	72-90	1	E:72-90

(no "Exon" information available for 1Z5Y)

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

    Alignment length:118
                                    36        46        56        66        76        86        96       106       116       126       136        
           DSBD_ECOLI    27 RSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGCADAGFCYPPETKTVPLSEVVAN 144
               SCOP domains d1z5yd_ D: Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)                                    SCOP domains
               CATH domains 1z5yD00 D:8-125  [code=2.60.40.1250, no name defined]                                                                  CATH domains
               Pfam domains DsbC-1z5yD01 D:8-121                                                                                              ---- 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
                 1z5y D   8 RSQFVPADQAFAFDFQQNQHDLNLTWQIKDGYYLYRKQIRITPEHAKIADVQLPQGVWHEDEFYGKSEIYRDRLTLPVTINQASAGATLTVTYQGSADAGFCYPPETKTVPLSEVVAN 125
                                    17        27        37        47        57        67        77        87        97       107       117

Chain E from PDB  Type:PROTEIN  Length:136
 aligned with DSBE_ECOLI | P0AA86 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:136
                                    58        68        78        88        98       108       118       128       138       148       158       168       178      
           DSBE_ECOLI    49 RLESLDNPGQFYQADVLTQGKPVLLNVWATWCPTCRAEHQYLNQLSAQGIRVVGMNYKDDRQKAISWLKELGNPYALSLFDGDGMLGLDLGVYGAPETFLIDGNGIIRYRHAGDLNPRVWEEEIKPLWEKYSKEAA 184
               SCOP domains d1z5ye1 E:49-184 Thioredoxin-like protein CcmG (CycY, DsbE)                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Redoxin-1z5yE01 E:49-173                                                                                                     ----------- Pfam domains
         Sec.struct. author .ee.......eehhhhhhh...eeeeee...hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeeee..hhhhhhh......eeeee.....eeeeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z5y E  49 RLESLDNPGQFYQADVLTQGKPVLLNVWATWCPTSRAEHQYLNQLSAQGIRVVGMNYKDDRQKAISWLKELGNPYALSLFDGDGMLGLDLGVYGAPETFLIDGNGIIRYRHAGDLNPRVWEEEIKPLWEKYSKEAA 184
                                    58        68        78        88        98       108       118       128       138       148       158       168       178

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

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

Escherichia coli. Organism_taxid: 562. (2)

1z5yD00

D:8-125

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Redoxin (27)

Escherichia coli (strain K12) (3)

Redoxin-1z5yE01

E:49-173

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

Family: DsbC (6)

Escherichia coli (strain K12) (5)

DsbC-1z5yD01

D:8-121

Asymmetric/Biological Unit(hide GO term definitions)

Chain D (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.

Chain E (DSBE_ECOLI | P0AA86)

molecular function
	GO:0015036	disulfide oxidoreductase activity	Catalysis of the reaction: substrate with reduced sulfide groups = substrate with oxidized disulfide bonds.
	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:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	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.
cellular component
	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:0031237	intrinsic component of periplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that penetrate the periplasmic side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala E:143 - Pro E:144	[ RasMol ]

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1se1	CRYSTAL STRUCTURE OF THE DISULFIDE-LINKED COMPLEX BETWEEN THE N-TERMINAL AND C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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