2HI7 - JenaLib

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Title :   CRYSTAL STRUCTURE OF DSBA-DSBB-UBIQUINONE COMPLEX

Authors :   K. Inaba, S. Murakami, M. Suzuki, A. Nakagawa, E. Yamashita, K. Okada, K. Ito

Date :   29 Jun 06 (Deposition) - 05 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.70

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

Keywords :   Disulfide Bond, Redox, Dsbb, Membrane Protein, Ubiquinone, Oxidative Protein Folding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Inaba, S. Murakami, M. Suzuki, A. Nakagawa, E. Yamashita, K. Okada, K. Ito
Crystal Structure Of The Dsbb-Dsba Complex Reveals A Mechanism Of Disulfide Bond Generation
Cell(Cambridge, Mass. ) V. 127 789 2006
PubMed-ID: 17110337 | Reference-DOI: 10.1016/J.CELL.2006.10.034
(for further references see the PDB file header)

Molecule 1
	Chains	:	A
	EC Number	:	1.8.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE70 (QIAGEN)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DSBA

Molecule 2 - DISULFIDE BOND FORMATION PROTEIN B
	Chains	:	B
	EC Number	:	1.8.5.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE70 (QIAGEN)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DSBB, DISULFIDE OXIDOREDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	UQ1	1	Ligand/Ion	UBIQUINONE-1
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	UQ1	1	Ligand/Ion	UBIQUINONE-1
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	UQ1	2	Ligand/Ion	UBIQUINONE-1
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:38 , HIS A:41	BINDING SITE FOR RESIDUE ZN A 190
2	AC2	SOFTWARE	ALA B:29 , LYS B:39 , CYS B:41 , LEU B:43 , CYS B:44 , GLU B:47 , ARG B:48 , HIS B:91 , MET B:142 , LEU B:146	BINDING SITE FOR RESIDUE UQ1 B 501

Asymmetric Unit

No.	Residues
1	A:30	-	B:104
2	B:41	-	B:44

Asymmetric Unit

No.	Residues
1	Val A:150	-	Pro A:151

(no "SAP(SNP)/Variant" information available for 2HI7)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBA_ECOLI	41-59	1	A:22-40

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBA_ECOLI	41-59	1	A:22-40

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBA_ECOLI	41-59	2	A:22-40

(no "Exon" information available for 2HI7)

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:188
 aligned with DSBA_ECOLI | P0AEG4 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:188
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199        
           DSBA_ECOLI    20 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 207
               SCOP domains d2hi7a1 A:1-188 Disulfide-bond formation facilitator (DsbA)                                                                                                                                  SCOP domains
               CATH domains 2hi7A00 A:1-188 Glutaredoxin                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..........eeeee...hhhhhhhhhh.hhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhh......eeee...eee.hhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hi7 A   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    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:134
 aligned with DSBB_ECOLI | P0A6M2 from UniProtKB/Swiss-Prot  Length:176

    Alignment length:149
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153         
           DSBB_ECOLI    14 AWLLMAFTALALELTALWFQHVMLLKPCVLCIYERCALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVASGDCAERQWDFLGLEMPQWLLGIFIAYLIVAVLVVI 162
               SCOP domains d2hi7b1 B:14-162 Disulfide bond formation protein DsbB                                                                                                SCOP domains
               CATH domains 2hi7B00 B:14-162 DsbB-like                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhh..hhhhh---------------hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hi7 B  14 AWLLMAFTALALELTALWFQHVMLLKPCVLCIYERVALFGVLGAALIGAIAPKTPLRYVAMVIWLYSAFRGVQLTYEHTMLQLYPSPFATCDFMVRFPEWLPLDKWVPQVFVA---------------MPQWLLGIFIAYLIVAVLVVI 162
                                    23        33        43        53        63        73        83        93       103       113       123  |      -       143       153         
                                                                                                                                          126             142

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Bromodomain-like (339)

Superfamily: DsbB-like (1)

Family: DsbB-like (1)

Protein domain: Disulfide bond formation protein DsbB (1)

Escherichia coli [TaxId: 562] (1)

d2hi7b1

B:14-162

Class: Alpha and beta proteins (a/b) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: DsbA-like (29)

Protein domain: Disulfide-bond formation facilitator (DsbA) (17)

Escherichia coli [TaxId: 562] (15)

d2hi7a1

A:1-188

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Escherichia coli. Organism_taxid: 562. (18)

2hi7A00

A:1-188

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Bromodomain-like (2)

Homologous Superfamily: DsbB-like (2)

Escherichia coli. Organism_taxid: 562. (1)

2hi7B00

B:14-162

(no "Pfam Domain" information available for 2HI7)

Asymmetric Unit(hide GO term definitions)

Chain A (DSBA_ECOLI | P0AEG4)

molecular function
	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:0003756	protein disulfide isomerase activity	Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
	GO:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0071236	cellular response to antibiotic	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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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: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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain B (DSBB_ECOLI | P0A6M2)

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: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:0015035	protein disulfide oxidoreductase activity	Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
	GO:0022900	electron transport chain	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: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:0009408	response to heat	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 heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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: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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	2hi7
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(no "Related Entries Specified in the PDB File" available for 2HI7)

Description

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SS Bonds (2, 2)

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