35EXOc

3'-5' exonuclease

• SMART accession number: SM00474
• Description: 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
• Interpro abstract (IPR002562):

  This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [ (PUBMED:9697700) ].

  Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction [ (PUBMED:9288107) (PUBMED:9224595) ]. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homologue of the WRN protein [ (PUBMED:9697700) ]. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome.

• GO process: nucleobase-containing compound metabolic process (GO:0006139)
• GO function: nucleic acid binding (GO:0003676), 3'-5' exonuclease activity (GO:0008408)

There are 40504 35EXOc domains in 40484 proteins in SMART's nrdb database.

Cellular role (predicted cellular role)

Cellular role: replication

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Brautigam CA, Sun S, Piccirilli JA, Steitz TA
• Structures of normal single-stranded DNA and deoxyribo-3'-S-phosphorothiolates bound to the 3'-5' exonucleolytic active site of DNA polymerase I from Escherichia coli.
• Biochemistry. 1999; 38: 696-704

The interaction of a divalent metal ion with a leaving 3' oxygen is a central component of several proposed mechanisms of phosphoryl transfer. In support of this are recent kinetic studies showing that thiophilic metal ions (e.g., Mn2+) stimulate the hydrolysis of compounds in which sulfur takes the place of the leaving oxygen. To examine the structural basis of this phenomenon, we have solved four crystal structures of single-stranded DNA's containing either oxygen or sulfur at a 3'-bridging position bound in conjunction with various metal ions at the 3'-5' exonucleolytic active site of the Klenow fragment (KF) of DNA polymerase I from Escherichia coli. Two structures of normal ssDNA bound to KF in the presence of Zn2+ and Mn2+ or Zn2+ alone were refined at 2.6- and 2.25-A resolution, respectively. They serve as standards for comparison with other Mn2+- and Zn2+-containing structures. In these cases, Mn2+ and Zn2+ bind at metal ion site B in a nearly identical position to Mg2+ (Brautigam and Steitz (1998) J. Mol. Biol. 277, 363-377). Two structures of KF bound to a deoxyoligonucleotide that contained a 3'-bridging sulfur at the scissile phosphate were refined at 2.03-A resolution. Although the bridging sulfur compounds bind in a manner very similar to that of the normal oligonucleotides, the presence of the sulfur changes the metal ion binding properties of the active site such that Mn2+ and Zn2+ are observed at metal ion site B, but Mg2+ is not. It therefore appears that the ability of the bridging sulfur compounds to exclude nonthiophilic metal ions from metal ion site B explains the low activity of KF exonuclease on these substrates in the presence of Mg2+ (Curley et al. (1997) J. Am. Chem. Soc. 119, 12691-12692) and that the 3'-bridging atom of the substrate is influencing the binding of metal ion B prior to catalysis.

• Moser MJ, Holley WR, Chatterjee A, Mian IS
• The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains.
• Nucleic Acids Res. 1997; 25: 5110-8

Prior sequence analysis studies have suggested that bacterial ribonuclease (RNase) Ds comprise a complete domain that is found also in Homo sapiens polymyositis-scleroderma overlap syndrome 100 kDa autoantigen and Werner syndrome protein. This RNase D 3'-->5' exoribonuclease domain was predicted to have a structure and mechanism of action similar to the 3'-->5' exodeoxyibonuclease (proofreading) domain of DNA polymerases. Here, hidden Markov model (HMM) and phylogenetic studies have been used to identify and characterise other sequences that may possess this exonuclease domain. Results indicate that it is also present in the RNase T family; Borrelia burgdorferi P93 protein, an immunodominant antigen in Lyme disease; bacteriophage T4 dexA and Escherichia coli exonuclease I, processive 3'-->5' exodeoxyribonucleases that degrade single-stranded DNA; Bacillus subtilis dinG, a probable helicase involved in DNA repair and possibly replication, and peptide synthase 1; Saccharomyces cerevisiae Pab1p-dependent poly(A) nuclease PAN2 subunit, required for shortening mRNA poly(A) tails; Caenorhabditis elegans and Mus musculus CAF1, transcription factor CCR4-associated factor 1; Xenopus laevis XPMC2, prevention of mitotic catastrophe in fission yeast; Drosophila melanogaster egalitarian, oocyte specification and axis determination, and exuperantia, establishment of oocyte polarity; H.sapiens HEM45, expressed in tumour cell lines and uterus and regulated by oestrogen; and 31 open reading frames including one in Methanococcus jannaschii . Examination of a multiple sequence alignment and two three-dimensional structures of proofreading domains has allowed definition of the core sequence, structural and functional elements of this exonuclease domain.

• Braithwaite DK, Ito J
• Compilation, alignment, and phylogenetic relationships of DNA polymerases.
• Nucleic Acids Res. 1993; 21: 787-802

• Ollis DL, Brick P, Hamlin R, Xuong NG, Steitz TA
• Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.
• Nature. 1985; 313: 762-6

The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine monophosphate. The most striking feature of the larger domain is a deep crevice of the appropriate size and shape for binding double-stranded B-DNA. A flexible subdomain may allow the enzyme to surround completely the DNA substrate, thereby allowing processive nucleotide polymerization without enzyme dissociation.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
33.33	map00240	Pyrimidine metabolism
33.33	map03030	DNA replication
33.33	map00230	Purine metabolism

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with 35EXOc domain which could be assigned to a KEGG orthologous group, and not all proteins containing 35EXOc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of 35EXOc domains in PDB

PDB code	Title
1d8y	CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA
1d9d	CRYSTALL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH SHORT DNA FRAGMENT CARRYING 2'-0-AMINOPROPYL-RNA MODIFICATIONS 5'-D(TCG)-AP(AUC)-3'
1d9f	CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3'
1dpi	STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP
1kfd	CRYSTAL STRUCTURES OF THE KLENOW FRAGMENT OF DNA POLYMERASE I COMPLEXED WITH DEOXYNUCLEOSIDE TRIPHOSPHATE AND PYROPHOSPHATE
1kfs	DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX
1kln	DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX
1krp	DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX
1ksp	DNA POLYMERASE I KLENOW FRAGMENT (E.C.2.7.7.7) MUTANT/DNA COMPLEX
1l3s	Crystal Structure of Bacillus DNA Polymerase I Fragment complexed to 9 base pairs of duplex DNA.
1l3t	Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 10 base pairs of duplex DNA following addition of a single dTTP residue
1l3u	Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 11 base pairs of duplex DNA following addition of a dTTP and a dATP residue.
1l3v	Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 15 base pairs of duplex DNA following addition of dTTP, dATP, dCTP, and dGTP residues.
1l5u	Crystal Structure of Bacillus DNA Polymerase I Fragment product complex with 12 base pairs of duplex DNA following addition of a dTTP, a dATP, and a dCTP residue.
1lv5	Crystal Structure of the Closed Conformation of Bacillus DNA Polymerase I Fragment Bound to DNA and dCTP
1njw	GUANINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1njx	THYMINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1njy	THYMINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1njz	CYTOSINE-THYMINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1nk0	ADENINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1nk4	GUANINE-GUANINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1nk5	ADENINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1nk6	CYTOSINE-CYTOSINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1nk7	GUANINE-ADENINE MISMATCH AT THE POLYMERASE ACTIVE SITE
1nk8	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP.
1nk9	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER TWO ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP AND DGTP.
1nkb	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER THREE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, AND DTTP.
1nkc	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A GUANINE-THYMINE MISMATCH AFTER FIVE ROUNDS OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP, DGTP, DTTP, AND DATP.
1nke	A BACILLUS DNA POLYMERASE I PRODUCT COMPLEX BOUND TO A CYTOSINE-THYMINE MISMATCH AFTER A SINGLE ROUND OF PRIMER EXTENSION, FOLLOWING INCORPORATION OF DCTP.
1qsl	KLENOW FRAGMENT COMPLEXED WITH SINGLE-STRANDED SUBSTRATE AND EUROPIUM (III) ION
1u45	8oxoguanine at the pre-insertion site of the polymerase active site
1u47	cytosine-8-Oxoguanine base pair at the polymerase active site
1u48	Extension of a cytosine-8-oxoguanine base pair
1u49	Adenine-8oxoguanine mismatch at the polymerase active site
1u4b	Extension of an adenine-8oxoguanine mismatch
1ua0	Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase
1ua1	Structure of aminofluorene adduct paired opposite cytosine at the polymerase active site.
1xc9	Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication
1xwl	BACILLUS STEAROTHERMOPHILUS (NEWLY IDENTIFIED STRAIN AS YET UNNAMED) DNA POLYMERASE FRAGMENT
1yt3	Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing
2bdp	CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 9 BASE PAIRS OF DUPLEX DNA
2e6l	structure of mouse WRN exonuclease domain
2e6m	structure of mouse werner exonuclease domain
2fbt	WRN exonuclease
2fbv	WRN exonuclease, Mn complex
2fbx	WRN exonuclease, Mg complex
2fby	WRN exonuclease, Eu complex
2fc0	WRN exonuclease, Mn dGMP complex
2hbj	Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain
2hbk	Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn
2hbl	Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and AMP
2hbm	Structure of the yeast nuclear exosome component, Rrp6p, reveals an interplay between the active site and the HRDC domain; Protein in complex with Mn, Zn, and UMP
2hhq	O6-methyl-guanine:T pair in the polymerase-10 basepair position
2hhs	O6-methyl:C pair in the polymerase-10 basepair position
2hht	C:O6-methyl-guanine pair in the polymerase-2 basepair position
2hhu	C:O6-methyl-guanine in the polymerase postinsertion site (-1 basepair position)
2hhv	T:O6-methyl-guanine in the polymerase-2 basepair position
2hhw	ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation
2hhx	O6-methyl-guanine in the polymerase template preinsertion site
2hvh	ddCTP:O6MeG pair in the polymerase active site (0 position)
2hvi	ddCTP:G pair in the polymerase active site (0 position)
2hw3	T:O6-methyl-guanine pair in the polymerase postinsertion site (-1 basepair position)
2kfn	KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND MANGANESE
2kfz	KLENOW FRAGMENT WITH BRIDGING-SULFUR SUBSTRATE AND ZINC ONLY
2kzm	KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC AND MANGANESE
2kzz	KLENOW FRAGMENT WITH NORMAL SUBSTRATE AND ZINC ONLY
2xo7	Crystal structure of a dA:O-allylhydroxylamine-dC basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
2xy5	Crystal structure of an artificial salen-copper basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
2xy6	Crystal structure of a salicylic aldehyde basepair in complex with fragment DNA polymerase I from Bacillus stearothermophilus
2xy7	Crystal structure of a salicylic aldehyde base in the pre-insertion site of fragment DNA polymerase I from Bacillus stearothermophilus
2y1i	Crystal structure of a S-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase I from Bacillus stearothermophilus
2y1j	Crystal structure of a R-diastereomer analogue of the spore photoproduct in complex with fragment DNA polymerase I from Bacillus stearothermophilus
3bdp	DNA POLYMERASE I/DNA COMPLEX
3cym	Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis
3eyz	Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form)
3ez5	Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA , dCTP, and zinc (closed form).
3hp6	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch
3hpo	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S mutant bound to G:T mismatch
3ht3	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus V713P mutant bound to G:dCTP
3pv8	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation
3px0	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation
3px4	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation
3px6	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (tautomer) in Closed Conformation
3saf	Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
3sag	Crystal structure of the human RRP6 catalytic domain with D313N mutation in the active site
3sah	Crystal structure of the human RRP6 catalytic domain with Y436A mutation in the catalytic site
3tan	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-1) Position
3tap	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-3) Position
3taq	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-4) Position
3tar	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-6) Position
3thv	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddATP-dT in Closed Conformation
3ti0	Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddGTP-dC in Closed Conformation
4b9l	Structure of the high fidelity DNA polymerase I with the oxidative formamidopyrimidine-dA DNA lesion in the pre-insertion site.
4b9m	Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dA DNA lesion -thymine basepair in the post- insertion site.
4b9n	Structure of the high fidelity DNA polymerase I correctly bypassing the oxidative formamidopyrimidine-dA DNA lesion.
4b9s	Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion outside of the pre-insertion site.
4b9t	Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion -dC basepair in the post-insertion site.
4b9u	Structure of the high fidelity DNA polymerase I with an oxidative formamidopyrimidine-dG DNA lesion -dA basepair in the post-insertion site.
4b9v	Structure of the high fidelity DNA polymerase I with extending from an oxidative formamidopyrimidine-dG DNA lesion -dA basepair.
4bdp	CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES
4dqi	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and dCTP (paired with dG of template)
4dqp	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and ddCTP (paired with dG of template)
4dqq	Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+
4dqr	Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mn2+
4dqs	Binary complex of Bacillus DNA Polymerase I Large Fragment and duplex DNA with rC in primer terminus paired with dG of template
4ds4	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mn2+
4ds5	Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+
4dse	Ternary complex of Bacillus DNA Polymerase I Large Fragment F710Y, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+
4dsf	Ternary complex of Bacillus DNA Polymerase I Large Fragment F710Y, DNA duplex, and rCTP (paired with dG of template) in presence of Mn2+
4dsi	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, Se-dGTP and Calcium
4dsj	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, dGTP and Calcium
4dsk	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA, PPi and Calcium
4dsl	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with duplex DNA and Calcium
4dwi	Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus with self complementary DNA, Se-dGTP and Calcium
4e0d	Binary complex of Bacillus DNA Polymerase I Large Fragment E658A and duplex DNA
4ez6	Bacillus DNA Polymerase I Large Fragment Complex 1
4ez9	Bacillus DNA Polymerase I Large Fragment Complex 2
4f2r	DNA Polymerase I Large Fragment complex 3
4f2s	DNA Polymerase I Large Fragment complex 4
4f3o	DNA Polymerase I Large Fragment Complex 5
4f4k	DNA Polymerase I Large Fragment Complex 6
4f8r	Bacillus DNA Polymerase I Large Fragment complex 7
4nlb	Crystal structure of the catalytic core of RRP6 from Trypanosoma brucei
4nlc	Crystal structure of the catalytic core of RRP6 from Trypanosoma brucei, mutant C496S
4o0i	4O0I
4oo1	4OO1
4uqg	4UQG
4yfu	4YFU
5c0w	5C0W
5c0x	5C0X
5c0y	5C0Y
5dkt	5DKT
5dku	5DKU
5fiq	5FIQ
5fis	5FIS
5k36	5K36

Links (links to other resources describing this domain)

• PFAM: 3_5_exonuclease
• INTERPRO: IPR002562