2B6M - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF THE DSBA MUTANT (P31A-C33A)

Authors :   C. Vives, A. Royant, L. Serre

Date :   03 Oct 05 (Deposition) - 17 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   Disulfide; Thioredoxin; Thiol-Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Vives, A. Royant, L. Serre
Structure Of The Dsba Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DSBA, DSF, PPFA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DSBA

		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	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:31 , GLN A:35 , THR B:168 , MET B:171	BINDING SITE FOR RESIDUE PEG A 190
2	AC2	SOFTWARE	THR A:168 , MET A:171 , ALA B:31 , GLN B:35	BINDING SITE FOR RESIDUE PEG A 191

Asymmetric Unit

No.	Residues
1	A:30	-	B:30

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2B6M)

Asymmetric Unit (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 B: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, 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	- B:22-40

(no "Exon" information available for 2B6M)

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:187
 aligned with DSBA_ECOLI | P0AEG4 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:187
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
           DSBA_ECOLI    21 QYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 207
               SCOP domains d2b6ma_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains 2b6mA00 A:2-188 Glutaredoxin                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeee....hhhhhhhhh.hhhhhhhhh......eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...ee.hhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b6m A   2 QYEDGKQYTTLEKPVAGAPQVLEFFSFFCAHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B 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 d2b6mb_ B: automated matches                                                                                                                                                                 SCOP domains
               CATH domains 2b6mB00 B:1-188 Glutaredoxin                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeee.......hhhhhh.hhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...ee.hhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b6m B   1 AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCAHAYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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) (23833)

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: DsbA-like (29)

Protein domain: automated matches (10)

Escherichia coli [TaxId: 562] (1)

1a	d2b6ma_	A:
1b	d2b6mb_	B:

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)

Escherichia coli. Organism_taxid: 562. (43)

1a	2b6mA00	A:2-188
1b	2b6mB00	B:1-188

(no "Pfam Domain" information available for 2B6M)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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).

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:150 - Pro A:151	[ RasMol ]
		Val B:150 - Pro B:151	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2b6m
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1dsb	WILD TYPE DSBA
1ti1	DSBA MUTANT C33A
1u3a	DSBA MUTANT C33A
2b3s	DSBA MUTANT P31G/C33A

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

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Exons (0, 0)

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Gene Ontology (8, 8)

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