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(-) Description

Title :  DBR1 IN COMPLEX WITH SYNTHETIC LINEAR RNA
 
Authors :  E. J. Montemayor, A. Katolik, N. E. Clark, A. B. Taylor, J. P. Schuermann D. J. Combs, R. Johnsson, S. P. Holloway, S. W. Stevens, M. J. Damha, P. J
Date :  23 Apr 14  (Deposition) - 27 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,V,W,X,Y,Z
Biol. Unit 1:  A,V  (1x)
Biol. Unit 2:  B,W  (1x)
Biol. Unit 3:  C,X  (1x)
Biol. Unit 4:  D,Y  (1x)
Biol. Unit 5:  E,Z  (1x)
Keywords :  Nuclease, Phosphodiesterase, Metallohydrolase, Metallophosphoesterase, Lariat Rna, Hydrolase, Metalloenzyme, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Montemayor, A. Katolik, N. E. Clark, A. B. Taylor, J. P. Schuermann, D. J. Combs, R. Johnsson, S. P. Holloway, S. W. Stevens, M. J. Damha, P. J. Hart
Structural Basis Of Lariat Rna Recognition By The Intron Debranching Enzyme Dbr1.
Nucleic Acids Res. V. 42 10845 2014
PubMed-ID: 25123664  |  Reference-DOI: 10.1093/NAR/GKU725

(-) Compounds

Molecule 1 - RNA LARIAT DEBRANCHING ENZYME, PUTATIVE
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: YEP351
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: EHI_062730
    Mutation: YES
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759
 
Molecule 2 - RNA (5'-R(*CP*UP*AP*(A2P)P*AP*CP*AP*A)-3')
    Chains: V, W, X, Y, Z
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEVWXYZ
Biological Unit 1 (1x): A    V    
Biological Unit 2 (1x):  B    W   
Biological Unit 3 (1x):   C    X  
Biological Unit 4 (1x):    D    Y 
Biological Unit 5 (1x):     E    Z

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1A2P5Mod. NucleotideADENOSINE-2'-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MN5Ligand/IonMANGANESE (II) ION
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1A2P1Mod. NucleotideADENOSINE-2'-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1A2P1Mod. NucleotideADENOSINE-2'-5'-DIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4SO42Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1A2P1Mod. NucleotideADENOSINE-2'-5'-DIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4SO43Ligand/IonSULFATE ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1A2P1Mod. NucleotideADENOSINE-2'-5'-DIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 2)
No.NameCountTypeFull Name
1A2P1Mod. NucleotideADENOSINE-2'-5'-DIPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:45 , ASN A:90 , HIS A:180 , HIS A:230 , A2P V:501 , HOH V:701binding site for residue MN A 401
02AC2SOFTWAREARG A:50 , ASN A:95 , HIS A:99 , PRO A:146 , HOH A:502 , HOH A:508 , HOH A:678binding site for residue SO4 A 402
03AC3SOFTWAREGLN A:163 , SER A:298 , ILE A:299 , SER A:300 , HOH A:622binding site for residue GOL A 403
04AC4SOFTWAREASP B:45 , ASN B:90 , HIS B:180 , HIS B:230 , A2P W:501 , HOH W:701binding site for residue MN B 401
05AC5SOFTWARELYS A:320 , TYR B:51 , TYR B:74 , HOH B:600 , HOH B:656binding site for residue SO4 B 402
06AC6SOFTWAREARG B:50 , ASN B:95 , HIS B:99 , HOH B:536 , HOH B:603 , HOH B:619 , HOH B:631binding site for residue SO4 B 403
07AC7SOFTWAREASP C:45 , ASN C:90 , HIS C:180 , HIS C:230 , HOH C:725 , A2P X:501binding site for residue MN C 401
08AC8SOFTWARETHR B:307 , LYS B:308 , LYS C:215binding site for residue SO4 C 402
09AC9SOFTWAREARG C:50 , ASN C:95 , HIS C:99 , HOH C:501 , HOH C:598 , HOH C:689binding site for residue SO4 C 403
10AD1SOFTWARELYS C:18 , TYR C:64 , HOH C:710 , A2P X:501binding site for residue SO4 C 404
11AD2SOFTWAREASP D:45 , ASN D:90 , HIS D:180 , HIS D:230 , HOH D:691 , A2P Y:501binding site for residue MN D 401
12AD3SOFTWAREARG D:50 , ASN D:95 , HIS D:99 , PRO D:146 , HOH D:509 , HOH D:522 , HOH D:583 , HOH D:677binding site for residue SO4 D 402
13AD4SOFTWAREASP E:45 , ASN E:90 , HIS E:180 , HIS E:230 , A2P Z:501 , HOH Z:703binding site for residue MN E 401
14AD5SOFTWAREARG E:50 , ASN E:95 , HIS E:99 , HOH E:555 , HOH E:584 , HOH E:615binding site for residue SO4 E 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Tyr A:144 -Pro A:145
2Phe A:292 -Pro A:293
3Tyr B:144 -Pro B:145
4Phe B:292 -Pro B:293
5Tyr C:144 -Pro C:145
6Phe C:292 -Pro C:293
7Tyr D:144 -Pro D:145
8Phe D:292 -Pro D:293
9Tyr E:144 -Pro E:145
10Phe E:292 -Pro E:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PEH)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhh.....eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhh........hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4peh A   5 QIQHIAIVGSVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344         


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4peh B   5 QIQHIAIVGSVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344         


Chain C from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee............ee................hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4peh C   5 QIQHIAIVGSVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344         


Chain D from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhh.....eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhh........hhhhhhh.........eee......hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4peh D   5 QIQHIAIVGSVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344         


Chain E from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhh.......hhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4peh E   5 QIQHIAIVGSVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344         


Chain V from PDB  Type:DNA/RNA  Length:4
                                    
                 4peh V 500 AxCA 503
                             |  
                           501-A2P


Chain W from PDB  Type:DNA/RNA  Length:5
                                     
                 4peh W 500 AxCAA 504
                             |   
                             |   
                           501-A2P


Chain X from PDB  Type:DNA/RNA  Length:6
                                      
                 4peh X 499 UAxCAA 504
                              |   
                              |   
                            501-A2P


Chain Y from PDB  Type:DNA/RNA  Length:5
                                     
                 4peh Y 500 AxCAA 504
                             |   
                             |   
                           501-A2P


Chain Z from PDB  Type:DNA/RNA  Length:4
                                    
                 4peh Z 500 AxCA 503
                             |  
                             |  
                           501-A2P
   Legend:   → Mismatch (orange background)
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  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 4PEH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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 Related Entries

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        C4M1P9_ENTHI | C4M1P9: 4pef 4peg 4pei 5k71 5k73 5k77 5k78

(-) Related Entries Specified in the PDB File

4pef 4peg 4pei