3U3Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   MOUSE TREX1 D200H MUTANT

Authors :   S. L. Bailey, S. Harvey, F. W. Perrino, T. Hollis

Date :   06 Oct 11 (Deposition) - 28 Dec 11 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.28

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

Keywords :   Rnase H Fold, 3' Exonuclease, Homodimer, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. L. Bailey, S. Harvey, F. W. Perrino, T. Hollis
Defects In Dna Degradation Revealed In Crystal Structures O Trex1 Exonuclease Mutations Linked To Autoimmune Disease.
Dna Repair V. 11 65 2012
PubMed-ID: 22071149 | Reference-DOI: 10.1016/J.DNAREP.2011.10.007

Molecule 1 - THREE PRIME REPAIR EXONUCLEASE 1
	Chains	:	B, A
	EC Number	:	3.1.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET28
	Gene	:	TREX1
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	3'-5' EXONUCLEASE TREX1

*Molecule 2 - 5'-D(GPAPCPG)-3'*
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	CHEMICALLY SYNTHESIZED DNA OLIGONUCLEOTIDE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	BU1	1	Ligand/Ion	1,4-BUTANEDIOL
2	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:192 , ASP A:193 , GLU A:198 , GLY A:199 , LEU A:202 , THR A:203 , HOH A:387	BINDING SITE FOR RESIDUE BU1 A 315
2	AC2	SOFTWARE	ASP A:18 , HOH A:344 , HOH A:349 , DC C:3 , DG C:4	BINDING SITE FOR RESIDUE CA C 5
3	AC3	SOFTWARE	ASP B:18 , HOH B:331 , HOH B:355 , HOH B:386 , DC D:3 , DG D:4	BINDING SITE FOR RESIDUE CA D 5

(no "SS Bond" information available for 3U3Y)

Asymmetric/Biological Unit

No.	Residues
1	His B:53	-	Pro B:54
2	Gln B:117	-	Pro B:118
3	Gln A:51	-	Gly A:52
4	His A:53	-	Pro A:54
5	Gln A:117	-	Pro A:118

(no "SAP(SNP)/Variant" information available for 3U3Y)

(no "PROSITE Motif" information available for 3U3Y)

(no "Exon" information available for 3U3Y)

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:215
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:229
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225         
          TREX1_MOUSE     6 LPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee..hhhhh..eeeeeeeeeehhhhh-----..............eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhh.---------....hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u3y A   6 LPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALE-----QGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQ---------RKSYSLGSIYTRLYWQAPTDSHTAEGHVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    15        25        35        45     |  55        65        75        85        95       105       115       125       135       145       155        |-       175       185       195       205       215       225         
                                                                  45    51                                                                                                              164       174

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:229
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225         
          TREX1_MOUSE     6 LPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh--................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh..-------....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u3y B   6 LPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALEN--ISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS-------RKSYSLGSIYTRLYWQAPTDSHTAEGHVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    15        25        35        45|  |    55        65        75        85        95       105       115       125       135       145       155       165|      175       185       195       205       215       225         
                                                                   46 49                                                                                                                  166     174

Chain C from PDB  Type:DNA  Length:4
                                    
                 3u3y C   1 GACG   4

Chain D from PDB  Type:DNA  Length:4
                                    
                 3u3y D   1 GACG   4

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 '\|'

(no "SCOP Domain" information available for 3U3Y)

(no "CATH Domain" information available for 3U3Y)

(no "Pfam Domain" information available for 3U3Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TREX1_MOUSE | Q91XB0)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0008296	3'-5'-exodeoxyribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a DNA molecule.
	GO:0032405	MutLalpha complex binding	Interacting selectively and non-covalently with the mismatch repair complex MutLalpha.
	GO:0032407	MutSalpha complex binding	Interacting selectively and non-covalently with the mismatch repair complex MutSalpha.
	GO:0032558	adenyl deoxyribonucleotide binding	Interacting selectively and non-covalently with an adenyl deoxyribonucleotide, any compound consisting of adenosine esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the deoxyribose moiety.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0008853	exodeoxyribonuclease III activity	Catalysis of the degradation of double-stranded DNA. It acts progressively in a 3' to 5' direction, releasing 5'-phosphomononucleotides.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006259	DNA metabolic process	Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
	GO:0035458	cellular response to interferon-beta	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 an interferon-beta stimulus. Interferon-beta is a type I interferon.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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
		BU1	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
		Gln A:117 - Pro A:118	[ RasMol ]
		Gln A:51 - Gly A:52	[ RasMol ]
		Gln B:117 - Pro B:118	[ RasMol ]
		His A:53 - Pro A:54	[ RasMol ]
		His B:53 - Pro B:54	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3u3y
		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
	TREX1_MOUSE \| Q91XB0
		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)
	3.1.11.2
		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

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
	TREX1_MOUSE \| Q91XB0
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	TREX1_MOUSE \| Q91XB0	:	2ioc 2o4g 2o4i 2oa8 3b6o 3b6p 3mxi 3mxj 3mxm 3u6f 4ynq

(no "Related Entries Specified in the PDB File" available for 3U3Y)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (24, 24)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File