2H72 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THIOREDOXIN MUTANT E85D IN HEXAGONAL (P61) SPACE GROUP

Authors :   J. A. Gavira, R. Godoy-Ruiz, B. Ibarra-Molero, J. M. Sanchez-Ruiz

Date :   01 Jun 06 (Deposition) - 15 May 07 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

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

Reference :   R. Godoy-Ruiz, J. A. Gavira, B. Ibarra-Molero, J. M. Sanchez-Ruiz
Crystal Structure Of Thioredoxin Mutant E85D In Hexagonal (P61) Space Group
To Be Published
PubMed: search

Molecule 1 - THIOREDOXIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTK100
	Expression System Strain	:	JF521
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRXA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		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, 3)

No.	Name	Count	Type	Full Name
1	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:73 , HOH A:532 , TRP B:31	BINDING SITE FOR RESIDUE MPD A 501
2	AC2	SOFTWARE	ALA A:19 , ALA A:22 , LEU A:53 , THR A:54	BINDING SITE FOR RESIDUE MPD A 502

Asymmetric Unit

No.	Residues
1	A:32	-	A:35
2	B:32	-	B:35

Asymmetric Unit

No.	Residues
1	Ile A:75	-	Pro A:76
2	Ile B:75	-	Pro B:76

(no "SAP(SNP)/Variant" information available for 2H72)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	2	A:24-42 B:24-42

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	A:24-42 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOREDOXIN_1	PS00194	Thioredoxin family active site.	THIO_ECOLI	25-43	1	- B:24-42

(no "Exon" information available for 2H72)

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:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    12        22        32        42        52        62        72        82        92       102       
           THIO_ECOLI     3 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA 109
               SCOP domains d2h72a_ A: Thioredoxin                                                                                      SCOP domains
               CATH domains 2h72A00 A:2-108 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh....eeeeee......hhhhh......eeeeee..eeeeeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOREDOXIN_1      ------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2h72 A   2 DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGDVAATKVGALSKGQLKEFLDANLA 108
                                    11        21        31        41        51        61        71        81        91       101

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with THIO_ECOLI | P0AA25 from UniProtKB/Swiss-Prot  Length:109

    Alignment length:107
                                    11        21        31        41        51        61        71        81        91       101       
           THIO_ECOLI     2 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANL 108
               SCOP domains d2h72b_ B: Thioredoxin                                                                                      SCOP domains
               CATH domains 2h72B00 B:1-107 Glutaredoxin                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhh.....eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh.....eeeeee..ee........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2h72 B   1 SDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGDVAATKVGALSKGQLKEFLDANL 107
                                    10        20        30        40        50        60        70        80        90       100

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: Thioltransferase (167)

Protein domain: Thioredoxin (106)

Escherichia coli [TaxId: 562] (47)

1a	d2h72a_	A:
1b	d2h72b_	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	2h72A00	A:2-108
1b	2h72B00	B:1-107

(no "Pfam Domain" information available for 2H72)

Asymmetric Unit(hide GO term definitions)

Chain A,B (THIO_ECOLI | P0AA25)

molecular function
	GO:0016671	oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
	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:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0034599	cellular response to oxidative stress	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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	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.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000103	sulfate assimilation	The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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