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(-) Description

Title :  HIGH-GLYCOSYLATION CRYSTAL STRUCTURE OF THE BIFUNCTIONAL ENDONUCLEASE (ATBFN2) FROM ARABIDOPSIS THALIANA
 
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 :  03 Apr 14  (Deposition) - 23 Jul 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, 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

Molecule 1 - ENDONUCLEASE 2
    Chains: A, B
    EC Number: 3.1.30.1
    Engineered: YES
    Expression System: ARABIDOPSIS THALIANA
    Expression System Common: THALE CRESS
    Expression System Taxid: 3702
    Fragment: RESIDUES 28-290
    Organism Common: THALE CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATENDO2, DEOXYRIBONUCLEASE ENDO2, SINGLE-STRANDED-NUCLEATE ENDONUCLEASE ENDO2, BIFUNCTIONAL ENDONUCLEASE ATBFN2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 26)

Asymmetric Unit (4, 26)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN6Ligand/IonZINC ION
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:45 , HIS A:58 , HIS A:120 , ASP A:124 , ZN A:433 , HOH A:2002 , HOH A:2058BINDING SITE FOR RESIDUE ZN A 431
02AC2SOFTWAREHIS A:130 , HIS A:154 , ASP A:158 , HOH A:2001 , HOH A:2132BINDING SITE FOR RESIDUE ZN A 432
03AC3SOFTWARETRP A:1 , HIS A:6 , ASP A:124 , ZN A:431 , HOH A:2002BINDING SITE FOR RESIDUE ZN A 433
04AC4SOFTWAREASP B:45 , HIS B:58 , HIS B:120 , ASP B:124 , ZN B:433 , HOH B:2043BINDING SITE FOR RESIDUE ZN B 431
05AC5SOFTWAREHIS B:130 , HIS B:154 , ASP B:158 , HOH B:2001 , HOH B:2118BINDING SITE FOR RESIDUE ZN B 432
06AC6SOFTWARETRP B:1 , HIS B:6 , ASP B:124 , ZN B:431BINDING SITE FOR RESIDUE ZN B 433
07AC7SOFTWAREHIS 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 , GLN A:108 , TYR A:109 , HOH A:2123 , HOH A:2214 , HOH A:2217 , HOH A:2218 , HOH A:2219 , HOH A:2220 , THR B:148 , ARG B:149 , LYS B:150BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 301 THROUGH MAN A 305 BOUND TO ASN A 91
08AC8SOFTWAREPRO A:30 , TRP A:43 , ASN A:110 , GLU A:113 , HOH A:2047 , HOH A:2222 , HOH A:2223 , HOH A:2225BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 331 THROUGH NAG A 332 BOUND TO ASN A 110
09AC9SOFTWARETYR A:170 , LEU A:181 , ASN A:184 , GLU A:188 , TRP A:189 , TYR A:244 , HOH A:2168 , HOH A:2204 , HOH A:2229 , HOH A:2230 , HOH A:2232BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A 361 THROUGH NAG A 362 BOUND TO ASN A 184
10BC1SOFTWARETHR A:148 , LYS A:150 , HIS B:52 , TRP B:53 , ARG B:83 , ALA B:88 , ASN B:91 , TYR B:92 , GLN B:95 , GLN B:108 , TYR B:109 , HOH B:2112 , HOH B:2192 , HOH B:2195 , HOH B:2197 , HOH B:2198 , HOH B:2199 , HOH B:2200BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 301 THROUGH MAN B 305 BOUND TO ASN B 91
11BC2SOFTWAREPRO B:30 , ARG B:50 , ASN B:110 , GLU B:113 , GLU B:234 , HOH B:2110 , HOH B:2180 , HOH B:2203 , HOH B:2204BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 331 THROUGH BMA B 333 BOUND TO ASN B 110
12BC3SOFTWAREGLU B:31 , TYR B:170 , ALA B:180 , LEU B:181 , ASN B:184 , GLU B:188 , TRP B:189 , TYR B:244 , HOH B:2143 , HOH B:2156 , HOH B:2205 , HOH B:2206 , HOH B:2207 , HOH B:2209 , HOH B:2210BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 361 THROUGH BMA B 363 BOUND TO ASN B 184

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:10 -A:41
2A:66 -A:218
3A:74 -A:84
4A:199 -A:205
5B:10 -B:41
6B:66 -B:218
7B:74 -B:84
8B:199 -B:205

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CWM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CWM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CWM)

(-) Exons   (0, 0)

(no "Exon" information available for 4CWM)

(-) Sequences/Alignments

Asymmetric 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 .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhheee......hhhhhh.........hhhhhhhhhhhhhh...------...hhhhhhhhhhhhhhhhhhhh.eee.hhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...-..hhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cwm 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                                                             


Chain B 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 .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhheee......hhhhhh.........hhhhhhhhhhhhhh...------...hhhhhhhhhhhhhhhhhhhh.eee.hhhhhh..eeee..eeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...-..hhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cwm B   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)

(no "SCOP Domain" information available for 4CWM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CWM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CWM)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  4cwm
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  3.1.30.1
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 Related Entries

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UniProtKB/Swiss-Prot
        ENDO2_ARATH | Q9C9G4: 3w52 4cxo 4cxp 4cxv

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