1TJD - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF THE REDUCED DISULPHIDE BOND ISOMERASE, DSBC, FROM ESCHERICHIA COLI

Authors :   K. Banaszak, I. Mechin, G. Frost, W. Rypniewski

Date :   04 Jun 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Dimer, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Banaszak, I. Mechin, G. Frost, W. Rypniewski
Structure Of The Reduced Disulfide-Bond Isomerase Dsbc From Escherichia Coli.
Acta Crystallogr. , Sect. D V. 60 1747 2004
PubMed-ID: 15388920 | Reference-DOI: 10.1107/S0907444904018359
(for further references see the PDB file header)

Molecule 1
	Chains	:	A
	EC Number	:	5.3.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDM801
	Expression System Strain	:	BL21 (DE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DSBC, XPRA, B2893, Z4231, ECS3765
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1TJD)

Asymmetric Unit

No.	Residues
1	A:141	-	A:163

Asymmetric Unit

No.	Residues
1	Gly A:49	-	Pro A:50
2	Thr A:182	-	Pro A:183

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	DSBC_ECO57	36-231	1	A:16-211
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	DSBC_ECOLI	36-231	1	A:16-211
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBC_ECO57	110-128	1	A:90-108
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBC_ECOLI	110-128	1	A:90-108

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	DSBC_ECO57	36-231	2	A:16-211
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	DSBC_ECOLI	36-231	2	A:16-211
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBC_ECO57	110-128	2	A:90-108
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	DSBC_ECOLI	110-128	2	A:90-108

(no "Exon" information available for 1TJD)

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:216
 aligned with DSBC_ECO57 | P0AEG7 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:216
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           DSBC_ECO57    21 DDAAIQQTLAKMGIKSSDIQPAPVAGMKTVLTNSGVLYITDDGKHIIQGPMYDVSGTAPVNVTNKMLLKQLNALEKEMIVYKAPQEKHVITVFTDITCGYCHKLHEQMADYNALGITVRYLAFPRQGLDSDAEKEMKAIWCAKDKNKAFDDVMAGKSVAPASCDVDIADHYALGVQLGVSGTPAVVLSNGTLVPGYQPPKEMKEFLDEHQKMTSGK 236
               SCOP domains d1tjda2 A:1-60                                              d1tjda1 A:61-216 Disulfide bond isomerase, DsbC, C-terminal domain                                                                                           SCOP domains
               CATH domains 1tjdA01 A:1-61  [code=3.10.450.70, no name defined]          ----------------1tjdA02 A:78-216 Glutaredoxin                                                                                                               CATH domains
               Pfam domains ----DsbC_N-1tjdA02 A:5-58                                 ----------------------Thioredoxin_2-1tjdA01 A:81-206                                                                                                ---------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eeee.....eeeeee..eeeeee.....ee....ee......eehhhhhhhhhhhhhhhhheee......eeeeeee...hhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh..hhhhhhhhhhhh..........hhhhhhhhhhhh......eee.....eee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ---------------THIOREDOXIN_2  PDB: A:16-211 UniProt: 36-231                                                                                                                                                        ----- PROSITE (2)
                PROSITE (3) -----------------------------------------------------------------------------------------THIOREDOXIN_1      ------------------------------------------------------------------------------------------------------------ PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tjd A   1 DDAAIQQTLAKMGIKSSDIQPAPVAGMKTVLTNSGVLYITDDGKHIIQGPMYDVSGTAPVNVTNKMLLKQLNALEKEMIVYKAPQEKHVITVFTDITCGYCHKLHEQMADYNALGITVRYLAFPRQGLDSDAEKEMKAIWCAKDKNKAFDDVMAGKSVAPASCDVDIADHYALGVQLGVSGTPAVVLSNGTLVPGYQPPKEMKEFLDEHQKMTSGK 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain A from PDB  Type:PROTEIN  Length:216
 aligned with DSBC_ECOLI | P0AEG6 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:216
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      
           DSBC_ECOLI    21 DDAAIQQTLAKMGIKSSDIQPAPVAGMKTVLTNSGVLYITDDGKHIIQGPMYDVSGTAPVNVTNKMLLKQLNALEKEMIVYKAPQEKHVITVFTDITCGYCHKLHEQMADYNALGITVRYLAFPRQGLDSDAEKEMKAIWCAKDKNKAFDDVMAGKSVAPASCDVDIADHYALGVQLGVSGTPAVVLSNGTLVPGYQPPKEMKEFLDEHQKMTSGK 236
               SCOP domains d1tjda2 A:1-60                                              d1tjda1 A:61-216 Disulfide bond isomerase, DsbC, C-terminal domain                                                                                           SCOP domains
               CATH domains 1tjdA01 A:1-61  [code=3.10.450.70, no name defined]          ----------------1tjdA02 A:78-216 Glutaredoxin                                                                                                               CATH domains
               Pfam domains ----DsbC_N-1tjdA02 A:5-58                                 ----------------------Thioredoxin_2-1tjdA01 A:81-206                                                                                                ---------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....eeee.....eeeeee..eeeeee.....ee....ee......eehhhhhhhhhhhhhhhhheee......eeeeeee...hhhhhhhhhhhhhhhhh.eeeeeee.......hhhhhhhhhhhh..hhhhhhhhhhhh..........hhhhhhhhhhhh......eee.....eee...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------THIOREDOXIN_2  PDB: A:16-211 UniProt: 36-231                                                                                                                                                        ----- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) -----------------------------------------------------------------------------------------THIOREDOXIN_1      ------------------------------------------------------------------------------------------------------------ PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tjd A   1 DDAAIQQTLAKMGIKSSDIQPAPVAGMKTVLTNSGVLYITDDGKHIIQGPMYDVSGTAPVNVTNKMLLKQLNALEKEMIVYKAPQEKHVITVFTDITCGYCHKLHEQMADYNALGITVRYLAFPRQGLDSDAEKEMKAIWCAKDKNKAFDDVMAGKSVAPASCDVDIADHYALGVQLGVSGTPAVVLSNGTLVPGYQPPKEMKEFLDEHQKMTSGK 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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)

Escherichia coli. Organism_taxid: 562. (43)

1tjdA02

A:78-216

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.70, no name defined] (6)

Escherichia coli. Organism_taxid: 562. (5)

1tjdA01

A:1-61

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Thioredoxin_2 (5)

Escherichia coli O157:H7 (2)

Thioredoxin_2-1tjdA01

A:81-206

Clan: no clan defined [family: DsbC_N] (3)

Family: DsbC_N (3)

Escherichia coli O157:H7 (2)

DsbC_N-1tjdA02

A:5-58

Asymmetric Unit(hide GO term definitions)

Chain A (DSBC_ECOLI | P0AEG6)

molecular function
	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: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 A (DSBC_ECO57 | P0AEG7)

biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
cellular component
	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
(no "Ligands, Modified Residues, Ions" information available for 1tjd)

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

	Cis Peptide Bonds
		Gly A:49 - Pro A:50	[ RasMol ]
		Thr A:182 - Pro A:183	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1tjd
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	DSBC_ECOLI \| P0AEG6
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	5.3.4.1
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UniProtKB/Swiss-Prot
	DSBC_ECO57 \| P0AEG7	:	1eej 1g0t 1jzd 1jzo
	DSBC_ECOLI \| P0AEG6	:	1eej 1g0t 1jzd 1jzo 2iyj

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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