3W52 - JenaLib

Title :   ZINC-DEPENDENT BIFUNCTIONAL NUCLEASE

Authors :   T. L. Chou, T. P. Ko, C. Y. Ko, J. F. Shaw, A. H. J. Wang

Date :   18 Jan 13 (Deposition) - 17 Apr 13 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

Chains :   Asym./Biol. Unit : A

Keywords :   Mostly Alpha-Helical, Dna, Rna, Nuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. L. Chou, T. P. Ko, C. Y. Ko, T. Y. Lin, R. T. Guo, T. F. Yu, H. C. Chan, J. F. Shaw, A. H. J. Wang
Mechanistic Insights To Catalysis By A Zinc-Dependent Bi-Functional Nuclease From Arabidopsis Thaliana
Biocatal Agric Biotechnol 2013
PubMed: search | Reference-DOI: 10.1016/J.BCAB.2013.03.006

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:53 , LEU A:57 , GLY A:82 , ARG A:83 , ALA A:88 , ASN A:91 , TYR A:92 , GLN A:95 , NAG A:302 , HOH A:607 , HOH A:608 , HOH A:661	BINDING SITE FOR RESIDUE NAG A 301
02	AC2	SOFTWARE	TRP A:53 , ARG A:83 , NAG A:301 , BMA A:303 , HOH A:517 , HOH A:539 , HOH A:608 , HOH A:609 , HOH A:779	BINDING SITE FOR RESIDUE NAG A 302
03	AC3	SOFTWARE	NAG A:302 , HOH A:524 , HOH A:609 , HOH A:635 , HOH A:782	BINDING SITE FOR RESIDUE BMA A 303
04	AC4	SOFTWARE	TRP A:43 , ASN A:110 , GLU A:113 , NAG A:305 , HOH A:576 , HOH A:698 , HOH A:787 , HOH A:788 , HOH A:789	BINDING SITE FOR RESIDUE NAG A 304
05	AC5	SOFTWARE	PRO A:30 , NAG A:304 , SO4 A:313 , HOH A:513 , HOH A:514 , HOH A:577 , HOH A:787 , HOH A:843	BINDING SITE FOR RESIDUE NAG A 305
06	AC6	SOFTWARE	TYR A:170 , ALA A:180 , LEU A:181 , ASN A:184 , TRP A:189 , TYR A:244 , NAG A:307 , HOH A:552 , HOH A:553 , HOH A:554 , HOH A:623 , HOH A:755	BINDING SITE FOR RESIDUE NAG A 306
07	AC7	SOFTWARE	SER A:67 , GLN A:69 , NAG A:306 , HOH A:552 , HOH A:747 , HOH A:813 , HOH A:814 , HOH A:858 , HOH A:875	BINDING SITE FOR RESIDUE NAG A 307
08	AC8	SOFTWARE	TYR A:59 , ASN A:61 , LEU A:129 , LYS A:137 , GLY A:138 , ASN A:140 , HIS A:154 , HOH A:501 , HOH A:507 , HOH A:729 , HOH A:734	BINDING SITE FOR RESIDUE ADE A 308
09	AC9	SOFTWARE	ASP A:45 , HIS A:58 , HIS A:120 , ASP A:124 , ZN A:311 , SO4 A:312	BINDING SITE FOR RESIDUE ZN A 309
10	BC1	SOFTWARE	HIS A:130 , HIS A:154 , ASP A:158 , SO4 A:312 , HOH A:501	BINDING SITE FOR RESIDUE ZN A 310
11	BC2	SOFTWARE	TRP A:1 , HIS A:6 , ASP A:124 , ZN A:309 , SO4 A:312	BINDING SITE FOR RESIDUE ZN A 311
12	BC3	SOFTWARE	TRP A:1 , HIS A:6 , ASP A:45 , LYS A:48 , HIS A:58 , HIS A:120 , ASP A:124 , HIS A:130 , ASP A:158 , ZN A:309 , ZN A:310 , ZN A:311 , HOH A:501 , HOH A:506 , HOH A:507 , HOH A:772	BINDING SITE FOR RESIDUE SO4 A 312
13	BC4	SOFTWARE	TRP A:43 , ARG A:46 , ARG A:50 , NAG A:305 , HOH A:576 , HOH A:791	BINDING SITE FOR RESIDUE SO4 A 313
14	BC5	SOFTWARE	ARG A:149 , LYS A:150 , HOH A:771 , HOH A:864	BINDING SITE FOR RESIDUE SO4 A 314

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:256
 aligned with ENDO2_ARATH | Q9C9G4 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:263
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287   
          ENDO2_ARATH    28 WGKEGHEIICKIAQTRLDETAAKAVKELLPESAEGDLSSLCLWADRVKFRYHWSSPLHYINTPDACSYQYNRDCKDESGEKGRCVAGAIYNYTTQLLSYKTAASSQSQYNLTEALLFVSHFMGDIHQPLHVSYASDKGGNTIEVHWYTRKANLHHIWDSNIIETAEADLYNSALEGMVDALKKNITTEWADQVKRWETCTKKTACPDIYASEGIQAACDWAYKGVTEGDTLEDEYFYSRLPIVYQRLAQGGVRLAATLNRIFG 290
               SCOP domains d3w52a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhheee......hhhhhh.........hhhhhhhhhhhhhh...-------..hhhhhhhhhhhhhhhhhhhh.eee.hhh.....eeee..eeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w52 A   1 WGKEGHEIICKIAQTRLDETAAKAVKELLPESAEGDLSSLCLWADRVKFRYHWSSPLHYINTPDACSYQYNRDCKDESGEKGRCVAGAIYNYTTQLLSYK-------QYNLTEALLFVSHFMGDIHQPLHVSYASDKGGNTIEVHWYTRKANLHHIWDSNIIETAEADLYNSALEGMVDALKKNITTEWADQVKRWETCTKKTACPDIYASEGIQAACDWAYKGVTEGDTLEDEYFYSRLPIVYQRLAQGGVRLAATLNRIFG 263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
                                                                                                                             100     108

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 (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ENDO2_ARATH | Q9C9G4)

molecular function
	GO:0043765	T/G mismatch-specific endonuclease activity	Catalysis of the repair of T/G mismatches arising from deamination of 5-methylcytosine in DNA by nicking double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the mismatched thymidine residue. The incision is mismatch-dependent and strand-specific, in favor of the G-containing strand. The incision serves as a starting point for subsequent excision repair by DNA polymerase I, which excises thymidine and reinserts cytidine.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	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:0000014	single-stranded DNA endodeoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks.
biological process
	GO:0006308	DNA catabolic process	The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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