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(-) Description

Title :  CRYSTAL STRUCTURE OF MN2+ BOUND HUMAN APE1
 
Authors :  Q. Chen, H. He, M. M. Georgiadis
Date :  27 May 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Sandwich, Endonuclease, Dna-Binding, Nucleus, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. He, Q. Chen, M. M. Georgiadis
High-Resolution Crystal Structures Reveal Plasticity In The Metal Binding Site Of Apurinic/Apyrimidinic Endonuclease I.
Biochemistry V. 53 6520 2014
PubMed-ID: 25251148  |  Reference-DOI: 10.1021/BI500676P

(-) Compounds

Molecule 1 - DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
    Chains: A
    EC Number: 3.1.-.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 38-318
    Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APEX NUCLEASE, APEN, APURINIC-APYRIMIDINIC ENDONUCLEASE 1, AP ENDONUCLEASE 1, APE-1, REF-1, REDOX FACTOR-1, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, MITOCHONDRIAL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:186 , LYS A:227 , PRO A:234 , GLN A:235BINDING SITE FOR RESIDUE EDO A 401
2AC2SOFTWARESER A:115 , HIS A:116 , GLN A:117 , TYR A:118BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREPRO A:248 , SER A:288 , HIS A:289 , SER A:290 , HOH A:625BINDING SITE FOR RESIDUE EDO A 403
4AC4SOFTWAREHIS A:215 , GLU A:216 , ARG A:237 , GLN A:238 , GLY A:241BINDING SITE FOR RESIDUE EDO A 404
5AC5SOFTWARELEU A:62 , ASP A:90 , ILE A:91 , SER A:135 , ARG A:136 , GLN A:137BINDING SITE FOR RESIDUE EDO A 405
6AC6SOFTWARELYS A:78 , LEU A:104 , ALA A:106BINDING SITE FOR RESIDUE EDO A 406
7AC7SOFTWAREALA A:138 , LEU A:140 , PHE A:162 , ASP A:163BINDING SITE FOR RESIDUE EDO A 407
8AC8SOFTWAREASP A:70 , GLU A:96 , HOH A:598 , HOH A:599 , HOH A:600 , HOH A:601BINDING SITE FOR RESIDUE MN A 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QH9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:247 -Pro A:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QH9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QH9)

(-) Exons   (0, 0)

(no "Exon" information available for 4QH9)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eeeeeee..hhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhheeeee..........eeeee.....eeee...hhhhh....eeeee....eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhh..hhhhh.....hhhhhhhhhhhhhhh..eehhhhhh.........................eeeee.hhhhh.eeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qh9 A  38 ASEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL 318
                                    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       297       307       317
   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 4QH9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QH9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QH9)

(-) Gene Ontology  (65, 65)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Val A:247 - Pro A:248   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        APEX1_HUMAN | P27695: 1bix 1cqg 1cqh 1de8 1de9 1dew 1e9n 1hd7 2isi 2o3h 3u8u 4iem 4lnd 4qhd 4qhe 5cfg 5dff 5dfh 5dfi 5dfj 5dg0

(-) Related Entries Specified in the PDB File

4qhd 4qhe