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Title :   THE CRYSTAL STRUCTURE OF TREX1 EXPLAINS THE 3' NUCLEOTIDE SPECIFICITY AND REVEALS A POLYPROLINE II HELIX FOR PROTEIN PARTENRING

Authors :   U. De Silva, T. Hollis

Date :   10 Oct 06 (Deposition) - 20 Feb 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Proline Helix, Nucleotide Complex, Dnaq Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. De Silva, S. Choudhury, S. L. Bailey, S. Harvey, F. W. Perrino, T. Hollis
The Crystal Structure Of Trex1 Explains The 3' Nucleotide Specificity And Reveals A Polyproline Ii Helix For Protein Partnering.
J. Biol. Chem. V. 282 10537 2007
PubMed-ID: 17293595 | Reference-DOI: 10.1074/JBC.M700039200
(for further references see the PDB file header)

Molecule 1 - THREE PRIME REPAIR EXONUCLEASE 1
	Chains	:	B, A
	EC Number	:	3.1.11.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21*(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL FRAGMENT, RESIDUES 1-242
	Gene	:	TREX1
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	3'-5' EXONUCLEASE TREX1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	D5M	2	Ligand/Ion	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
2	MN	4	Ligand/Ion	MANGANESE (II) ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:18 , GLU B:20 , ASP B:200 , D5M B:303 , MN B:402	BINDING SITE FOR RESIDUE MN B 401
2	AC2	SOFTWARE	ASP B:18 , D5M B:303 , MN B:401 , HOH B:473 , HOH B:474 , HOH B:508 , HOH B:516	BINDING SITE FOR RESIDUE MN B 402
3	AC3	SOFTWARE	ASP A:18 , GLU A:20 , ASP A:200 , D5M A:302 , MN A:404	BINDING SITE FOR RESIDUE MN A 403
4	AC4	SOFTWARE	ASP A:18 , D5M A:302 , MN A:403 , HOH A:466 , HOH A:468 , HOH A:510	BINDING SITE FOR RESIDUE MN A 404
5	AC5	SOFTWARE	ASP A:18 , LEU A:19 , GLU A:20 , ALA A:21 , GLY A:23 , LEU A:24 , SER A:78 , ALA A:81 , ILE A:84 , THR A:85 , TYR A:129 , HIS A:195 , ASP A:200 , MN A:403 , MN A:404 , HOH A:410 , HOH A:448 , HOH A:466	BINDING SITE FOR RESIDUE D5M A 302
6	AC6	SOFTWARE	ASP B:18 , LEU B:19 , GLU B:20 , ALA B:21 , GLY B:23 , LEU B:24 , SER B:78 , GLY B:80 , ALA B:81 , ILE B:84 , THR B:85 , TYR B:129 , HIS B:195 , ASP B:200 , MN B:401 , MN B:402 , HOH B:404 , HOH B:437 , HOH B:441 , HOH B:474 , HOH B:500 , HOH B:508 , HOH B:516	BINDING SITE FOR RESIDUE D5M B 303

(no "SS Bond" information available for 2IOC)

Asymmetric/Biological Unit

No.	Residues
1	His B:53	-	Pro B:54
2	Gln B:117	-	Pro B:118
3	His A:50	-	Pro A:51
4	Gln A:117	-	Pro A:118

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

(no "PROSITE Motif" information available for 2IOC)

(no "Exon" information available for 2IOC)

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:218
 aligned with TREX1_MOUSE | Q91XB0 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:230
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234
          TREX1_MOUSE     5 TLPHGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d2ioca1 A:5-234 Three prime repair exonucl    ease 1, TREX1                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee..hhhhh..eeeeeeeeeehhhhh.----..............eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhhh.--------...hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ioc A   5 TLPHGHmQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALEN----QGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS--------KSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPmYG 234
                                  | 14        24        34        44 |    | 51       |64        74        84        94       104       114       124       134       144       154       164 |       -|      184       194       204       214       224       234
                                 11-MSE                             46   48         59|                                                                                                    166      175                                                      232-MSE
                                                                                     63

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

    Alignment length:227
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       
          TREX1_MOUSE     8 HGHMQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPSGNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
               SCOP domains d2iocb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhhh.-------....hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ioc B   8 HGHmQTLIFLDLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQAS-------RKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPmYG 234
                               |    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157        |-      |177       187       197       207       217       227    |  
                               |                                                                                                                                                        166     174                                                       232-MSE
                              11-MSE

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: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: automated matches (127)

Protein domain: automated matches (127)

Mouse (Mus musculus) [TaxId: 10090] (6)

d2iocb_

Family: DnaQ-like 3'-5' exonuclease (253)

Protein domain: Three prime repair exonuclease 1, TREX1 (6)

Mouse (Mus musculus) [TaxId: 10090] (6)

d2ioca1

A:5-234

(no "CATH Domain" information available for 2IOC)

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

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
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		His B:53 - Pro B:54	[ RasMol ]

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	TREX1_MOUSE \| Q91XB0	:	2o4g 2o4i 2oa8 3b6o 3b6p 3mxi 3mxj 3mxm 3u3y 3u6f 4ynq

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Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (6, 6)

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Cis Peptide Bonds (4, 4)

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