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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL POLY(A) POLYMERASE (PAPD1)
 
Authors :  Y. Bai, S. K. Srivastava, J. H. Chang, L. Tong
Date :  25 Nov 10  (Deposition) - 30 Mar 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleotidyl Transferase, Rnp-Type Rna Binding Domain, Poly(A) Polymerase, Mitochondria, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Bai, S. K. Srivastava, J. H. Chang, J. L. Manley, L. Tong
Structural Basis For Dimerization And Activity Of Human Papd1, A Noncanonical Poly(A) Polymerase.
Mol. Cell V. 41 311 2011
PubMed-ID: 21292163  |  Reference-DOI: 10.1016/J.MOLCEL.2011.01.013

(-) Compounds

Molecule 1 - POLY(A) RNA POLYMERASE
    Chains: A, B
    EC Number: 2.7.7.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 ROSETTA (DE3)
    Expression System Taxid: 562
    Gene: MTPAP, PAPD1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PAP, PAP-ASSOCIATED DOMAIN-CONTAINING PROTEIN 1, POLYNUCLEOTIDE ADENYLYLTRANSFERASE, TERMINAL URIDYLYLTRANSFERASE 1, TUTASE 1, MTPAP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 39)

Asymmetric/Biological Unit (2, 39)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2UNK27Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 3PQ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_027602Y221HPAPD1_HUMANPolymorphism17855118A/BY221H
2UniProtVAR_064907N478DPAPD1_HUMANDisease (SPAX4)267606900A/BX478D
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3PQ1)

(-) 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:355
 aligned with PAPD1_HUMAN | Q9NVV4 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:471
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531 
          PAPD1_HUMAN    62 RFSEMQNERREQAQRTVLIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTHTPSTAMETAIPFRSRFFNLKLKNQTSERSRVRSSNQLPRSNKQLFELLCYAESIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLDETRNLSAHKISGNFLMEFQVKNVPSERIATQKILSVLGECLDHFGPGCVGVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAHSLTSSIPGAWITNFSLTMMVIFFLQRRSPPILPTLDSLKTLADAEDKCVIEGNNCTFVRDLSRIKPSQNTETLELLLKEFFEYFGNFAFDKNSINIRQGREQNKPDSSPLYIQNPFETSLNISKNVSQSQLQKFVDLARESAWILQQEDTDRPSISSNRPWGLVSLLL 532
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeeee...---hhhhhhhhhhh....eeee....eeeeee..---.hhhhhh....-----------------.......---------------hhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeeeehhhh.........eeeeee..-----....ee.---.ee......hhhhhhhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....--....hhhhhhhhhhhhhhh..-------..hhhhhh..---------------------.....hhhhhhhhhhhhhhhh------------.....-----.....------------hhhhhhhhhhhhhhhhhhhhh.-----------...hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pq1 A  62 RFSEmQNERREQAQRTVLIHCPEK---NKFLKYLSQFGPINNHFFYESFGLYAVVEFC---SIGSLQNGTHT-----------------xxxxxxx---------------NKQLFELLCYAESIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDmAAAYFPDCIVRPFGSSVNTFGKLGCDLDmFLDLD-----SAHKISG---mEFQVKNVPSERIATQKILSVLGECLDHFGPGCVGVQKILNARCPLVRFSHQASGFQCALTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAHSLTSS--GAWITNFSLTmmVIFFLQRRS-------DSLKTLADAE---------------------SQNTETLELLLKEFFEYFGNF------------xxxxx-----xxxxx------------SQSQLQKFVDLARESAWILQQE-----------PWGLVSLLL 532
                                |   71        81   |   |91       101       111       | - |     131 |       -       151||||||   -         - |     181       191       201       211     | 221       231       241    |  251     | 261 |   | 271       281       291       301       311       321       331       341       351       361       | -|      381||     391|      401       | -         -       431       441       451         -  |||||  -  |||||  -       491       501       511|        -  |    531 
                                |                 85  89                           119 123       133               151-UNK||             173                                         217-MSE                      246-MSE1   257   263   |                                                                                                   369  |       382-MSE   392     400      409                   431                 451          464-UNK     ||478-UNK      491                  512         524        
                               66-MSE                                                                               152-UNK|                                                                                                           267-MSE                                                                                                  372        383-MSE                                                                           465-UNK    ||||                                                       
                                                                                                                     153-UNK                                                                                                                                                                                                                                                                                                                  466-UNK   ||||                                                       
                                                                                                                      154-UNK                                                                                                                                                                                                                                                                                                                  467-UNK  ||||                                                       
                                                                                                                       155-UNK                                                                                                                                                                                                                                                                                                                  468-UNK ||||                                                       
                                                                                                                        156-UNK                                                                                                                                                                                                                                                                                                                       474-UNK                                                      
                                                                                                                         157-UNK                                                                                                                                                                                                                                                                                                                       475-UNK                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                        476-UNK                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                         477-UNK                                                   


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with PAPD1_HUMAN | Q9NVV4 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:471
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531 
          PAPD1_HUMAN    62 RFSEMQNERREQAQRTVLIHCPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKESIGSLQNGTHTPSTAMETAIPFRSRFFNLKLKNQTSERSRVRSSNQLPRSNKQLFELLCYAESIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDMAAAYFPDCIVRPFGSSVNTFGKLGCDLDMFLDLDETRNLSAHKISGNFLMEFQVKNVPSERIATQKILSVLGECLDHFGPGCVGVQKILNARCPLVRFSHQASGFQCDLTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAHSLTSSIPGAWITNFSLTMMVIFFLQRRSPPILPTLDSLKTLADAEDKCVIEGNNCTFVRDLSRIKPSQNTETLELLLKEFFEYFGNFAFDKNSINIRQGREQNKPDSSPLYIQNPFETSLNISKNVSQSQLQKFVDLARESAWILQQEDTDRPSISSNRPWGLVSLLL 532
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------                -----------------     -------                                          -------------------------------------------------------------------------------   ---------  ---------------------------------------------------------------------------------------------------         -------------------                                       ----PAP_assoc-3pq1B                  01 B:436-4            -------------------------    ------------- Pfam domains (1)
           Pfam domains (2) ------------------------                -----------------     -------                                          -------------------------------------------------------------------------------   ---------  ---------------------------------------------------------------------------------------------------         -------------------                                       ----PAP_assoc-3pq1B                  02 B:436-4            -------------------------    ------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhheeeeee...----------------...eeee...eeeeee.-----hhhhhh.------------------------------------------hhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......eeeeehhhh.........eeeeee..---......ee.--..ee........hhhhhhhhhhhhhhhhhh....eeeeee......eeeee......eeeee....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh---------..hhhhhhhhhhhhhhh..---------------------------------------....hhhhhhhhhhhhh..------------------..........------------hhhhhhhhhhhhhhhhhhhhhhhhh----......hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pq1 B  62 RFSEmQNERREQAQRTVLIHCPEK----------------NNHFFYESFGLYAVVEF-----IGSLQNG------------------------------------------NKQLFELLCYAESIDDQLNTLLKEFQLTEENTKLRYLTCSLIEDmAAAYFPDCIVRPFGSSVNTFGKLGCDLDmFLDLD---NLSAHKISG--LmEFQVKNVPSERIATQKILSVLGECLDHFGPGCVGVQKILNARCPLVRFSHQASGFQCALTTNNRIALTSSELLYIYGALDSRVRALVFSVRCWARAH---------WITNFSLTmmVIFFLQRRS---------------------------------------QNTETLELLLKEFFEYFGN------------------xxxxxxxxxx------------SQSQLQKFVDLARESAWILQQEDTD----SSNRPWGLVSLLL 532
                                |   71        81   |     -         -|      111      |  -  |     |-         -         -         -         - |     181       191       201       211     | 221       231       241    |  251   |   261 |  || 271       281       291       301       311       321       331       341       351       361  |      -  |    381||     391|        -         -         -         -|      441        |-         -       471|||||||  -       491       501       511   |   521       531 
                               66-MSE             85              102             118   124   130                                        173                                         217-MSE                      246-MSE1 255     263  ||                                                                                              364       374     382-MSE   392                                     432               450                469-UNK||478-UNK      491                     515  520            
                                                                                                                                                                                                                                      266|                                                                                                                 383-MSE                                                                                470-UNK|||                                                       
                                                                                                                                                                                                                                       267-MSE                                                                                                                                                                                                     471-UNK||                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                    472-UNK|                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                     473-UNK                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                      474-UNK                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                                                       475-UNK                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                        476-UNK                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                         477-UNK
   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 3PQ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PQ1)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PAP_assoc] (2)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PAPD1_HUMAN | Q9NVV4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0002134    UTP binding    Interacting selectively and non-covalently with UTP, uridine 5'-triphosphate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004652    polynucleotide adenylyltransferase activity    Catalysis of the template-independent extension of the 3'- end of an RNA or DNA strand by addition of one adenosine molecule at a time. Cannot initiate a chain 'de novo'. The primer, depending on the source of the enzyme, may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071044    histone mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of histone messenger RNA (mRNA).
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  3pq1
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  PAPD1_HUMAN | Q9NVV4
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PQ1)