4CXP - JenaLib

Title :   STRUCTURE OF BIFUNCTIONAL ENDONUCLEASE (ATBFN2) FROM ARABIDOPSIS THALIANA IN COMPLEX WITH SULFATE

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 :   1.22

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, 23)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:45 , HIS A:58 , HIS A:120 , ASP A:124 , ZN A:933 , SO4 A:961	BINDING SITE FOR RESIDUE ZN A 931
02	AC2	SOFTWARE	HIS A:130 , HIS A:154 , ASP A:158 , SO4 A:961 , HOH A:2260	BINDING SITE FOR RESIDUE ZN A 932
03	AC3	SOFTWARE	TRP A:1 , HIS A:6 , ASP A:124 , ZN A:931 , SO4 A:961	BINDING SITE FOR RESIDUE ZN A 933
04	AC4	SOFTWARE	GLU A:27 , LEU A:28 , LEU A:29 , PRO A:30 , THR A:112 , NAG A:831 , NAG A:832 , FUC A:835 , HOH A:2256 , HOH A:2464	BINDING SITE FOR RESIDUE 1PE A 960
05	AC5	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:931 , ZN A:932 , ZN A:933 , HOH A:2001 , HOH A:2121 , HOH A:2123 , HOH A:2260	BINDING SITE FOR RESIDUE SO4 A 961
06	AC6	SOFTWARE	ARG A:149 , LYS A:150 , HOH A:2279 , HOH A:2287 , HOH A:2292	BINDING SITE FOR RESIDUE SO4 A 962
07	AC7	SOFTWARE	TRP A:43 , ARG A:46 , ARG A:50 , NAG A:832 , HOH A:2115 , HOH A:2117 , HOH A:2466 , HOH A:2495	BINDING SITE FOR RESIDUE SO4 A 963
08	AC8	SOFTWARE	GLU A:34 , GLY A:35 , ASP A:36 , TRP A:53 , LEU A:57 , GLY A:82 , ARG A:83 , ALA A:88 , ASN A:91 , TYR A:92 , GLN A:95 , GLN A:108 , ASP A:179 , LYS A:182 , LYS A:183 , GLY A:224 , HOH A:2229 , HOH A:2230 , HOH A:2257 , HOH A:2330 , HOH A:2335 , HOH A:2387 , HOH A:2437 , HOH A:2438 , HOH A:2439 , HOH A:2441 , HOH A:2442 , HOH A:2444 , HOH A:2445 , HOH A:2446 , HOH A:2447 , HOH A:2448 , HOH A:2449 , HOH A:2450 , HOH A:2452 , HOH A:2453 , HOH A:2454 , HOH A:2458 , HOH A:2460 , HOH A:2461 , HOH A:2463	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 801 THROUGH MAN A 808 BOUND TO ASN A 91
09	AC9	SOFTWARE	ARG A:16 , PRO A:30 , ASN A:110 , GLU A:113 , GLU A:197 , 1PE A:960 , SO4 A:963 , HOH A:2103 , HOH A:2464 , HOH A:2465 , HOH A:2466 , HOH A:2468 , HOH A:2469 , HOH A:2470 , HOH A:2471 , HOH A:2473 , HOH A:2474 , HOH A:2475 , HOH A:2476 , HOH A:2478 , HOH A:2479	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 831 THROUGH FUC A 835 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 , PRO A:241 , TYR A:244 , HOH A:2315 , HOH A:2345 , HOH A:2480 , HOH A:2481 , HOH A:2483 , HOH A:2484 , HOH A:2486 , HOH A:2487 , HOH A:2488 , HOH A:2489 , HOH A:2491	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 861 THROUGH BMA A 863 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:257
 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 .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhheee......hhhhhh.........hhhhhhhhhhhhhh...------...hhhhhhhhhhhhhhhhhhhh.eee.hhh.....eeee..eeeehhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...-..hhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cxp A   1 WGKEGHEIICKIAQTRLDETAAKAVKELLPESAEGDLSSLCLWADRVKFRYHWSSPLHYINTPDACSYQYNRDCKDESGEKGRCVAGAIYNYTTQLLSYK------SQYNLTEALLFVSHFMGDIHQPLHVSYASDKGGNTIEVHWYTRKANLHHIWDSNIIETAEADLYNSALEGMVDALKKNITTEWADQVKRWETCTK-TACPDIYASEGIQAACDWAYKGVTEGDTLEDEYFYSRLPIVYQRLAQGGVRLAATLNRIFGH 264
                                    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    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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