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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CPS-6 MUTANT Q130K
 
Authors :  J. L. J. Lin, H. S. Yuan
Date :  17 Jun 14  (Deposition) - 17 Jun 15  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Biol. Unit 6:  D  (1x)
Keywords :  Beta-Beta-Alpha Metal Motif, Endoribonuclease, Mitochondrial Membrane, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. J. Lin, A. Nakagawa, R. Skeen-Gaar, W. Z. Yang, P. Zhao, Z. Zhang, X. Ge, S. Mitani, D. Xue, H. S. Yuan
Oxidative Stress Impairs Cell Death By Repressing The Nuclease Activity Of Mitochondrial Endonuclease G
Cell Rep V. 16 279 2016
PubMed-ID: 27346342  |  Reference-DOI: 10.1016/J.CELREP.2016.05.090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDONUCLEASE G, MITOCHONDRIAL
    Chains: A, B, C, D
    EC Number: 3.1.30.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 64-302
    Gene: CPS-6, C41D11.8
    Mutation: YES
    Organism Common: ROUNDWORM
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: ENDO G, CED-3 PROTEASE SUPPRESSOR 6

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (1x): A   
Biological Unit 4 (1x):  B  
Biological Unit 5 (1x):   C 
Biological Unit 6 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:148 , ASN A:180 , HOH A:532 , HOH A:541 , HOH A:542 , HOH A:546BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASN B:180 , HOH B:540 , HOH B:555 , HOH B:559 , HOH B:560BINDING SITE FOR RESIDUE MG B 401
3AC3SOFTWAREASN C:180 , HOH C:535 , HOH C:536 , HOH C:539 , HOH C:541BINDING SITE FOR RESIDUE MG C 401
4AC4SOFTWAREASN D:180 , HOH D:523 , HOH D:524 , HOH D:525 , HOH D:530BINDING SITE FOR RESIDUE MG D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QN0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QN0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QN0)

(-) Exons   (0, 0)

(no "Exon" information available for 4QN0)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh......eee....eeeee....eeeeeeeee.hhhhh....hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeeeeeeee...ee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qn0 A  64 SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAGVDRKLCEFKPDITFPKKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
                                    73        83        93       103       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
                                                                          112|                                                                                                                                                                                            
                                                                           114                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........eee...eeeeee....eeeeeeeee...........hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeeeeeeee..eee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qn0 B  64 SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAEGVDRKLCEFKPDITFPKKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293         


Chain C from PDB  Type:PROTEIN  Length:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........eee....eeeee....eeeeeeeee.hhhhh....hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee........hhhhhhhhhhhhhh....eeeeeeee...ee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qn0 C  64 SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAGVDRKLCEFKPDITFPKKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
                                    73        83        93       103       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294        
                                                                          112|                                                                                                                                                                                            
                                                                           114                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.........eee...eeeeee....eeeeeeeee.hhhhh.....hhhhh........hhhhh.hhhhhh....eeee..hhhhh..hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh....eeeeeeee...ee.....eeeeeeee....ee...eeeeeeeeeee..eeeeeeeeee........hhhhhh.hhhhhhhhhh.......hhh.eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qn0 D  64 SRSAEIMKHGYPGFTNVRTYEDFVLSYDYKTRTAHWVCEHLTPERLKHAEGVDRKLCEFKPDITFPKKFLSQNTDYKCSGFDRGHLAAAGNHRKSQLAVDQTFYLSNMSPQVGRGFNRDKWNDLEMHCRRVAKKMINSYIITGPLYLPKLEGDGKKYIKYQVIGDNNVAVPTHFFKVALFEVTPGKFELESYILPNAVIEDTVEISKFHVPLDAVERSAGLEIFARLDPKSIVKENGAK 302
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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 4QN0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QN0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QN0)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NUCG_CAEEL | Q95NM6: 3s5b 5gkc 5gkp

(-) Related Entries Specified in the PDB File

3s5b ONE ADDITIONAL MUTATION Q130K WAS INTRODUCED