4CXO - JenaLib

Title :   BIFUNCTIONAL ENDONUCLEASE IN COMPLEX WITH SSDNA

Authors :   T. -F. Yu, M. Maestre-Reyna, C. -Y. Ko, T. -P. Ko, Y. -J. Sun, T. -Y. Lin, J. A. H. -J. Wang

Date :   08 Apr 14 (Deposition) - 23 Jul 14 (Release) - 28 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Endonucleases, Glycosylation, Ssdna Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Yu, M. Maestre-Reyna, C. Ko, T. Ko, Y. Sun, T. Lin, J. Shaw, A. H. Wang
Structural Insights Of The Ssdna Binding Site In The Multifunctional Endonuclease Atbfn2 From Arabidopsis Thaliana.
Plos One V. 9 05821 2014
PubMed-ID: 25157844 | Reference-DOI: 10.1371/JOURNAL.PONE.0105821

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 19)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:48 , TYR A:59 , ASN A:61 , LEU A:129 , HIS A:130 , LYS A:137 , ASN A:140 , HIS A:154 , ASP A:158 , ZN A:452 , SO4 A:461 , HOH A:2082 , HOH A:2089	BINDING SITE FOR RESIDUE TMP A 401
02	AC2	SOFTWARE	TYR A:70 , ASN A:71 , TYR A:90 , LYS A:201 , TMP A:431 , HOH A:2240 , HOH A:2317	BINDING SITE FOR RESIDUE D5M A 430
03	AC3	SOFTWARE	LYS A:81 , GLY A:82 , GLY A:87 , TYR A:90 , ASN A:91 , TYR A:109 , NAG A:301 , D5M A:430 , HOH A:2130 , HOH A:2319 , HOH A:2320	BINDING SITE FOR RESIDUE TMP A 431
04	AC4	SOFTWARE	ASP A:45 , HIS A:58 , HIS A:120 , ASP A:124 , ZN A:453 , SO4 A:461	BINDING SITE FOR RESIDUE ZN A 451
05	AC5	SOFTWARE	HIS A:130 , HIS A:154 , ASP A:158 , TMP A:401 , SO4 A:461	BINDING SITE FOR RESIDUE ZN A 452
06	AC6	SOFTWARE	TRP A:1 , HIS A:6 , ASP A:124 , ZN A:451 , SO4 A:461	BINDING SITE FOR RESIDUE ZN A 453
07	AC7	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 , TMP A:401 , ZN A:451 , ZN A:452 , ZN A:453 , HOH A:2001	BINDING SITE FOR RESIDUE SO4 A 461
08	AC8	SOFTWARE	GLU A:34 , GLY A:35 , ASP A:36 , HIS A:52 , TRP A:53 , LEU A:57 , GLY A:82 , ARG A:83 , ALA A:88 , ASN A:91 , TYR A:92 , GLN A:95 , TYR A:109 , TMP A:431 , HOH A:2129 , HOH A:2130 , HOH A:2131 , HOH A:2147 , HOH A:2153 , HOH A:2284 , HOH A:2285 , HOH A:2286 , HOH A:2288 , HOH A:2290 , HOH A:2292 , HOH A:2293 , HOH A:2294 , HOH A:2295	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 301 THROUGH MAN A 305 BOUND TO ASN A 91
09	AC9	SOFTWARE	ARG A:16 , PRO A:30 , ASN A:110 , GLU A:113 , GLU A:197 , HOH A:2052 , HOH A:2062 , HOH A:2296 , HOH A:2297 , HOH A:2298 , HOH A:2299 , HOH A:2300 , HOH A:2301 , HOH A:2302 , HOH A:2304 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 331 THROUGH MAN A 334 BOUND TO ASN A 110
10	BC1	SOFTWARE	SER A:67 , GLN A:69 , TYR A:170 , LEU A:181 , ASN A:184 , TRP A:189 , TYR A:244 , HOH A:2195 , HOH A:2217 , HOH A:2309 , HOH A:2310 , HOH A:2311 , HOH A:2312 , HOH A:2313 , HOH A:2314 , HOH A:2315	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 361 THROUGH MAN A 363 BOUND TO ASN A 184

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:264
                                                                                                                                                                                                                                                                                                290 
                                    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-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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
                 4cxo A   1 WGKEGHEIICKIAQTRLDETAAKAVKELLPESAEGDLSSLCLWADRVKFRYHWSSPLHYINTPDACSYQYNRDCKDESGEKGRCVAGAIYNYTTQLLSY-------SEYNLTEALLFVSHFMGDIHQPLHVSYASDKGGNTIEVHWYTRKANLHHIWDSNIIETAEADLYNSALEGMVDALKKNITTEWADQVKRWETCTK-TACPDIYASEGIQAACDWAYKGVTEGDTLEDEYFYSRLPIVYQRLAQGGVRLAATLNRIFGH 264
                                    10        20        30        40        50        60        70        80        90        |-      |110       120       130       140       150       160       170       180       190       200| |    210       220       230       240       250       260    
                                                                                                                             99     107                                                                                           201 |                                                             
                                                                                                                                                                                                                                    203

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 (0, 0)

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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