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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A.FULGIDUS CCA-ADDING ENZYME IN COMPLEX WITH A HUMAN MENBETA MINIHELIX ENDING IN CCACC AND AMPCPP
 
Authors :  C. -D. Kuhn, L. Joshua-Tor
Date :  03 Dec 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Protein-Rna Complex, Trna, Non-Coding Rna, Cca-Adding Enzyme, Nucleotidyltransferase, Ncrna, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. D. Kuhn, J. E. Wilusz, Y. Zheng, P. A. Beal, L. Joshua-Tor
On-Enzyme Refolding Permits Small Rna And Trna Surveillance By The Cca-Adding Enzyme.
Cell V. 160 644 2015
PubMed-ID: 25640237  |  Reference-DOI: 10.1016/J.CELL.2015.01.005

(-) Compounds

Molecule 1 - CCA-ADDING ENZYME
    ChainsA, C
    EC Number2.7.7.72
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22
    Expression System StrainBL21(DE3)RIPL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCCA, AF_2156
    Organism ScientificARCHAEOGLOBUS FULGIDUS
    Organism Taxid224325
    StrainATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
    SynonymCCA TRNA NUCLEOTIDYLTRANSFERASE,TRNA CCA-PYROPHOSPHORYLASE, TRNA ADENYLYL-/CYTIDYLYL- TRANSFERASE,TRNA NUCLEOTIDYLTRANSFERASE, TRNA-NT
 
Molecule 2 - HUMAN MENBETA MINIHELIX ENDING IN CCACC
    ChainsB, D
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
15GP3Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG2Ligand/IonMAGNESIUM ION
5TAR4Ligand/IonD(-)-TARTARIC ACID
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5TAR3Ligand/IonD(-)-TARTARIC ACID
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
3MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5TAR1Ligand/IonD(-)-TARTARIC ACID
Biological Unit 3 (4, 10)
No.NameCountTypeFull Name
15GP3Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5TAR4Ligand/IonD(-)-TARTARIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:46 , SER A:47 , ARG A:50 , GLU A:59 , ASP A:61 , THR A:130 , HIS A:133 , LYS A:152 , TYR A:161 , ARG A:224 , MG A:502 , HOH A:623 , HOH A:627 , HOH A:628 , HOH A:653 , A B:35 , C B:36 , C B:37 , HOH B:601binding site for residue APC A 501
02AC2SOFTWARESER A:47 , GLU A:59 , ASP A:61 , APC A:501binding site for residue MG A 502
03AC3SOFTWAREVAL A:200 , ARG A:209 , PHE A:215 , VAL A:217 , GLU A:222 , HOH A:670binding site for residue TAR A 503
04AC4SOFTWAREARG A:310 , GLU A:311 , ASN A:312 , ARG A:380 , HOH A:717binding site for residue TAR A 504
05AC5SOFTWAREARG A:93 , TYR A:94 , ILE A:288 , VAL A:289 , ASN A:292 , HOH A:730binding site for residue MES A 505
06AC6SOFTWAREHIS A:396 , G B:11 , G B:12 , C B:21 , C B:22binding site for residue TAR B 501
07AC7SOFTWAREU B:14 , G B:16 , A B:17 , U B:19binding site for residue 5GP B 502
08AC8SOFTWAREGLY A:346 , ASN A:354 , ARG A:373 , C B:15 , G B:16 , G B:18 , 5GP B:502binding site for residue GMP B 503
09AC9SOFTWARESER C:47 , ARG C:50 , GLU C:59 , ASP C:61 , THR C:130 , HIS C:133 , LYS C:152 , TYR C:161 , ARG C:224 , MG C:502 , HOH C:645 , HOH C:655 , A D:35 , C D:36 , C D:37binding site for residue APC C 501
10AD1SOFTWAREGLU C:59 , ASP C:61 , APC C:501binding site for residue MG C 502
11AD2SOFTWAREGLU C:311 , PHE C:342 , LYS C:381 , PHE C:382binding site for residue TAR C 503
12AD3SOFTWAREG D:16 , A D:17binding site for residue GMP D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X4V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X4V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X4V)

(-) Exons   (0, 0)

(no "Exon" information available for 4X4V)

(-) 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:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeehhhhhh.......eeeeeeee....hhhhhhhhhhhhhhhhh.eee........eeeee..eeeeeeeee.............hhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh..ee...hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4v A   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKDSNSSSV 443
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440   

Chain B from PDB  Type:RNA  Length:33
                                                                 
                 4x4v B   1 GGCGCUGCGGGGUUCGAGUCCCCGCAGGCCACC  37
                                    10        20      ||34   
                                                     27|     
                                                      32     

Chain C from PDB  Type:PROTEIN  Length:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeee.............eeeeeeee....hhhhhhhhhhhhhhhhh.eee........eeeee..eeeeeeeee............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee....eeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x4v C   3 VEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252    || 266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436 
                                                                                                                                                                                                                                                                                        257|                                                                                                                                                                               
                                                                                                                                                                                                                                                                                         262                                                                                                                                                                               

Chain D from PDB  Type:RNA  Length:26
                                                          
                 4x4v D   1 GGCGCUGGGUUCGACCCCGCGCCACC  37
                                 || 13   ||   25|     
                                 6|     17|   25|     
                                 10      20    32     

   Legend:   → Mismatch (orange background)
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    → 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 4X4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X4V)

(-) Gene Ontology  (17, 17)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCA_ARCFU | O281261r89 1r8a 1r8b 1r8c 1sz1 1tfw 1tfy 1uet 1ueu 1uev 2dr5 2dr7 2dr8 2dr9 2dra 2drb 2dvi 2zh1 2zh2 2zh3 2zh4 2zh5 2zh6 2zh7 2zh8 2zh9 2zha 2zhb 3ouy 3ov7 3ova 3ovb 3ovs 4x4n 4x4o 4x4p 4x4q 4x4r 4x4s 4x4t 4x4u

(-) Related Entries Specified in the PDB File

4x4n 4x4o 4x4p 4x4q 4x4r 4x4s 4x4t 4x4u 4x4w 4x4x