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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF THE K18G MUTANT OF THE THIOREDOXIN FROM ALICYCLOBACILLUS ACIDOCALDARIUS

Authors :   S. Bartolucci, G. De Simone, S. Galdiero, R. Improta, V. Menchise, C. Pedone, E. Pedone, M. Saviano

Date :   28 Jan 03 (Deposition) - 05 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Thermostability, Thioredoxin, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bartolucci, G. De Simone, S. Galdiero, R. Improta, V. Menchise, C. Pedone, E. Pedone, M. Saviano
An Integrated Structural And Computational Study Of The Thermostability Of Two Thioredoxin Mutants From Alicyclobacillus Acidocaldarius
J. Bacteriol. V. 185 4285 2003
PubMed-ID: 12837806 | Reference-DOI: 10.1128/JB.185.14.4285-4289.2003
(for further references see the PDB file header)

Molecule 1 - THIOREDOXIN
	Chains	:	A, B, C, D
	EC Number	:	1.8.1.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ALICYCLOBACILLUS ACIDOCALDARIUS
	Organism Taxid	:	405212
	Synonym	:	TRX

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1NSW)

Asymmetric/Biological Unit

No.	Residues
1	A:29	-	A:32
2	B:29	-	B:32
3	C:29	-	C:32
4	D:29	-	D:32

Asymmetric/Biological Unit

No.	Residues
1	Ile A:72	-	Pro A:73
2	Ile B:72	-	Pro B:73
3	Ile C:72	-	Pro C:73
4	Ile D:72	-	Pro D:73

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_2	PS51352	Thioredoxin domain profile.	THIO_ALIAC	1-105	4	A:1-105 B:1-105 C:1-105 D:1-105
2	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ALIAC	21-39	4	A:21-39 B:21-39 C:21-39 D:21-39

(no "Exon" information available for 1NSW)

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 A from PDB  Type:PROTEIN  Length:105
 aligned with THIO_ALIAC | P80579 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           THIO_ALIAC     1 ATMTLTDANFQQAIQGDKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
               SCOP domains d1nswa_ A: Thioredoxin                                                                                    SCOP domains
               CATH domains 1nswA00 A:1-105 Glutaredoxin                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: A:1-105 UniProt: 1-105                                                                PROSITE (1)
                PROSITE (2) --------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1nsw A   1 ATMTLTDANFQQAIQGDGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:105
 aligned with THIO_ALIAC | P80579 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           THIO_ALIAC     1 ATMTLTDANFQQAIQGDKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
               SCOP domains d1nswb_ B: Thioredoxin                                                                                    SCOP domains
               CATH domains 1nswB00 B:1-105 Glutaredoxin                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: B:1-105 UniProt: 1-105                                                                PROSITE (1)
                PROSITE (2) --------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1nsw B   1 ATMTLTDANFQQAIQGDGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:PROTEIN  Length:105
 aligned with THIO_ALIAC | P80579 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           THIO_ALIAC     1 ATMTLTDANFQQAIQGDKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
               SCOP domains d1nswc_ C: Thioredoxin                                                                                    SCOP domains
               CATH domains 1nswC00 C:1-105 Glutaredoxin                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhh....eeeeee...hhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: C:1-105 UniProt: 1-105                                                                PROSITE (1)
                PROSITE (2) --------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1nsw C   1 ATMTLTDANFQQAIQGDGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
                                    10        20        30        40        50        60        70        80        90       100

Chain D from PDB  Type:PROTEIN  Length:105
 aligned with THIO_ALIAC | P80579 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           THIO_ALIAC     1 ATMTLTDANFQQAIQGDKPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
               SCOP domains d1nswd_ D: Thioredoxin                                                                                    SCOP domains
               CATH domains 1nswD00 D:1-105 Glutaredoxin                                                                              CATH domains
           Pfam domains (1) Thioredoxin-1nswD01 D:1-103                                                                            -- Pfam domains (1)
           Pfam domains (2) Thioredoxin-1nswD02 D:1-103                                                                            -- Pfam domains (2)
           Pfam domains (3) Thioredoxin-1nswD03 D:1-103                                                                            -- Pfam domains (3)
           Pfam domains (4) Thioredoxin-1nswD04 D:1-103                                                                            -- Pfam domains (4)
         Sec.struct. author ..eee...hhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) THIOREDOXIN_2  PDB: D:1-105 UniProt: 1-105                                                                PROSITE (1)
                PROSITE (2) --------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1nsw D   1 ATMTLTDANFQQAIQGDGPVLVDFWAAWCGPCRMMAPVLEEFAEAHADKVTVAKLNVDENPETTSQFGIMSIPTLILFKGGRPVKQLIGYQPKEQLEAQLADVLQ 105
                                    10        20        30        40        50        60        70        80        90       100

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Thioredoxin fold (994)

Superfamily: Thioredoxin-like (992)

Family: Thioltransferase (167)

Protein domain: Thioredoxin (106)

Alicyclobacillus acidocaldarius, formerly Bacillus acidocaldarius [TaxId: 405212] (4)

1a	d1nswa_	A:
1b	d1nswc_	C:
1c	d1nswd_	D:
1d	d1nswb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Glutaredoxin (620)

Homologous Superfamily: Glutaredoxin (617)

Alicyclobacillus acidocaldarius. Organism_taxid: 405212. (3)

1a	1nswA00	A:1-105
1b	1nswB00	B:1-105
1c	1nswC00	C:1-105
1d	1nswD00	D:1-105

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thioredoxin (367)

Family: Thioredoxin (82)

Alicyclobacillus acidocaldarius (Bacillus acidocaldarius) (3)

1a	Thioredoxin-1nswD01	D:1-103
1b	Thioredoxin-1nswD02	D:1-103
1c	Thioredoxin-1nswD03	D:1-103
1d	Thioredoxin-1nswD04	D:1-103

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (THIO_ALIAC | P80579)

molecular function
	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:0006662	glycerol ether metabolic process	The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1nsw)

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

	Cis Peptide Bonds
		Ile A:72 - Pro A:73	[ RasMol ]
		Ile B:72 - Pro B:73	[ RasMol ]
		Ile C:72 - Pro C:73	[ RasMol ]
		Ile D:72 - Pro D:73	[ RasMol ]

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	1nsw
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	THIO_ALIAC \| P80579	:	1nw2 1quw 1rqm

1nwl
1quw	SOLUTION STRUCTURE OF THE THIOREDOXIN FROM BACILLUS ACIDOCALDARIUS
2trx	CRYSTAL STRUCTURE OF THIOREDOXIN FROM ESCHERICHIA COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

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