1SEN - JenaLib

Title :   ENDOPLASMIC RETICULUM PROTEIN RP19 O95881

Authors :   Z. -J. Liu, L. Chen, W. Tempel, A. Shah, D. Lee, T. A. Dailey, M. R. Mayer, J. P. Rose, D. C. Richardson, J. S. Richardson, H. A. Dailey, B. -C. Wang Southeast Collaboratory For Structural Genomics (Secsg)

Date :   17 Feb 04 (Deposition) - 13 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : A

Keywords :   Endoplasmic Reticulum, Rp19, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. -J. Liu, L. Chen, W. Tempel, A. Shah, D. Lee, J. P. Rose, D. C. Richardson, J. S. Richardson, B. -C. Wang
Endoplasmic Reticulum Protein Rp19
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - THIOREDOXIN-LIKE PROTEIN P19
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TLP19
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG HUMAN PROTEIN PRODUCTION GROUP (T.A. DAILEY, M. MAYER) UNDER THE DIRECTION OF H.A. DAILEY.
	Synonym	:	ENDOPLASMIC RETICULUM PROTEIN ERP19

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:66 , GLY A:67 , CL A:1003 , CL A:1004 , CL A:1005	BINDING SITE FOR RESIDUE PT A 1001
2	AC2	SOFTWARE	LYS A:123 , HOH A:270 , PT A:1001 , CL A:1004 , CL A:1005	BINDING SITE FOR RESIDUE CL A 1003
3	AC3	SOFTWARE	TRP A:65 , LYS A:123 , PT A:1001 , CL A:1003	BINDING SITE FOR RESIDUE CL A 1004
4	AC4	SOFTWARE	GLY A:67 , ALA A:68 , HIS A:87 , PT A:1001 , CL A:1003	BINDING SITE FOR RESIDUE CL A 1005
5	AC5	SOFTWARE	LYS A:63 , ASP A:96 , GLU A:97	BINDING SITE FOR RESIDUE PT A 1002

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (7, 7)

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000371626	1a	ENSE00001860135	chr1:52521843-52520672	1172	TXD12_HUMAN	1-33	33	1	A:30-33	4
1.2	ENST00000371626	2	ENSE00000915802	chr1:52507269-52507209	61	TXD12_HUMAN	33-53	21	1	A:33-53	21
1.4	ENST00000371626	4	ENSE00000835700	chr1:52494302-52494250	53	TXD12_HUMAN	53-71	19	1	A:53-71	19
1.5	ENST00000371626	5	ENSE00000835699	chr1:52493020-52492947	74	TXD12_HUMAN	71-95	25	1	A:71-95	25
1.6b	ENST00000371626	6b	ENSE00000835698	chr1:52490251-52490182	70	TXD12_HUMAN	96-119	24	1	A:96-119	24
1.7a	ENST00000371626	7a	ENSE00000835697	chr1:52489246-52489163	84	TXD12_HUMAN	119-147	29	1	A:119-147	29
1.8c	ENST00000371626	8c	ENSE00001455699	chr1:52486684-52485803	882	TXD12_HUMAN	147-172	26	1	A:147-164	18

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
	(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:135
 aligned with TXD12_HUMAN | O95881 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:135
                                    39        49        59        69        79        89        99       109       119       129       139       149       159     
          TXD12_HUMAN    30 LGKGFGDHIHWRTLEDGKKEAAASGLPLMVIIHKSWCGACKALKPKFAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPRILFLDPSGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERLTGDAFR 164
               SCOP domains d1sena_ A: Thioredoxin-like protein p19, TLP19                                                                                          SCOP domains
               CATH domains 1senA00 A:30-164 Glutaredoxin                                                                                                           CATH domains
               Pfam domains ---------Thioredoxin_7-1senA01 A:39-120                                                    -------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhh..hhhhh.......eeeee........................hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------THIOREDOXIN_1      ---------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a-------------------Exon 1.4           ------------------------Exon 1.6b  PDB: A:96-119---------------------------Exon 1.8c          Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:33-5-----------------Exon 1.5  PDB: A:71-95   -----------------------Exon 1.7a  PDB: A:119-147    ----------------- Transcript 1 (2)
                 1sen A  30 LGKGFGDHIHWRTLEDGKKEAAASGLPLMVIIHKSWCGACKALKPKFAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPRILFLDPSGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERLTGDAFR 164
                                    39        49        59        69        79        89        99       109       119       129       139       149       159

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 (1, 1)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TXD12_HUMAN | O95881)

molecular function
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0015037	peptide disulfide oxidoreductase activity	Catalysis of the reaction: a peptide with reduced sulfide groups = a peptide with oxidized disulfide bonds.
	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:0019153	protein-disulfide reductase (glutathione) activity	Catalysis of the reaction: 2 glutathione + protein-disulfide = oxidized glutathione + protein-dithiol.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:1902236	negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of an endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway.
	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: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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:112 - Pro A:113	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1sen
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TXD12_HUMAN \| O95881
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TXD12_HUMAN \| O95881
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description