3UJ1 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE THIRD THIOREDOXIN DOMAIN OF HUMAN ERP46

Authors :   C. Parthier, A. Funkner, D. M. Ferrari, M. T. Stubbs

Date :   07 Nov 11 (Deposition) - 07 Nov 12 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym./Biol. Unit : A

Keywords :   Thioredoxin Fold, Protein Disulfide Isomerase, Protein Folding, Endoplasmic Reticulum, Substrate Binding, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Funkner, C. Parthier, M. Schutkowski, J. Zerweck, H. Lilie, N. Gyrych, G. Fischer, M. T. Stubbs, D. M. Ferrari
Peptide Binding By Catalytic Domains Of The Protein Disulfide Isomerase-Related Protein Erp46.
J. Mol. Biol. V. 425 1340 2013
PubMed-ID: 23376096 | Reference-DOI: 10.1016/J.JMB.2013.01.029

Compounds

Molecule 1 - THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23
	Expression System Strain	:	ROSETTA (DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 323-432
	Gene	:	TLP46, TXNDC5, UNQ364/PRO700
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ENDOPLASMIC RETICULUM RESIDENT PROTEIN 46, ER PROTEIN 46, ERP46, THIOREDOXIN-LIKE PROTEIN P46

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (3, 3)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000379757	1	ENSE00001482400	chr6:7911047-7910747	301	TXND5_HUMAN	1-88	88	0	-	-
1.3	ENST00000379757	3	ENSE00002035816	chr6:7904956-7904807	150	TXND5_HUMAN	88-138	51	0	-	-
1.4b	ENST00000379757	4b	ENSE00002030712	chr6:7899914-7899809	106	TXND5_HUMAN	138-173	36	0	-	-
1.5b	ENST00000379757	5b	ENSE00002020031	chr6:7895435-7895339	97	TXND5_HUMAN	174-206	33	0	-	-
1.6	ENST00000379757	6	ENSE00002062288	chr6:7891969-7891854	116	TXND5_HUMAN	206-244	39	0	-	-
1.7	ENST00000379757	7	ENSE00002051337	chr6:7889814-7889728	87	TXND5_HUMAN	245-273	29	0	-	-
1.8c	ENST00000379757	8c	ENSE00002072823	chr6:7889081-7888938	144	TXND5_HUMAN	274-321	48	0	-	-
1.9	ENST00000379757	9	ENSE00002061487	chr6:7886276-7886194	83	TXND5_HUMAN	322-349	28	1	A:323-349	27
1.10	ENST00000379757	10	ENSE00002026226	chr6:7884721-7884592	130	TXND5_HUMAN	349-392	44	1	A:349-392 (gaps)	44
1.11c	ENST00000379757	11c	ENSE00001964269	chr6:7883499-7881750	1750	TXND5_HUMAN	393-432	40	1	A:393-428	36

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:99
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:106
                                   332       342       352       362       372       382       392       402       412       422      
          TXND5_HUMAN   323 TVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
               SCOP domains d3uj1a_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....hhhhhhhh.eeeeeee...hhhhhhhhhhhhhhh.-------.eeeeeee...hhhhhhhh......eeeeee..eeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------THIOREDOXIN_1      -------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --------------------------Exon 1.10  PDB: A:349-392 (gaps)            Exon 1.11c  PDB: A:393-428           Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:323-349   ------------------------------------------------------------------------------- Transcript 1 (2)
                 3uj1 A 323 TVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSK-------GVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQA 428
                                   332       342       352       362  |      -|      382       392       402       412       422      
                                                                    365     373

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TXND5_HUMAN | Q8NBS9)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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.
biological process
	GO:0043277	apoptotic cell clearance	The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	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:0034976	response to endoplasmic reticulum 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 a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005788	endoplasmic reticulum lumen	The volume enclosed by the membranes of the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043202	lysosomal lumen	The volume enclosed within the lysosomal membrane.

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	Cis Peptide Bonds
		Tyr A:396 - Pro A:397	[ RasMol ]

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