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(-) Description

Title :  DIMERIC ARCHAEAL CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR WITH N-TERMINAL KH DOMAINS (KH-CPSF) FROM METHANOSARCINA MAZEI
 
Authors :  B. Mir-Montazeri, M. Ammelburg, D. Forouzan, A. N. Lupas, M. D. Hartman
Date :  08 Sep 10  (Deposition) - 06 Oct 10  (Release) - 15 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Hydrolase, Metallo-Beta-Lactamase, Beta-Casp, Rna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Mir-Montazeri, M. Ammelburg, D. Forouzan, A. N. Lupas, M. D. Hartmann
Crystal Structure Of A Dimeric Archaeal Cleavage And Polyadenylation Specificity Factor.
J. Struct. Biol. V. 173 191 2011
PubMed-ID: 20851187  |  Reference-DOI: 10.1016/J.JSB.2010.09.013

(-) Compounds

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 100 KD SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: METHANOSARCINA MAZEI
    Organism Taxid: 2209
    Synonym: ARCHAEAL CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR WITH N-TERMINAL KH DOMAINS, KH-CPSF

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:242 , HIS A:244 , HIS A:329 , ASP A:352 , ZN A:1639BINDING SITE FOR RESIDUE ZN A1638
2AC2SOFTWAREASP A:246 , HIS A:247 , ASP A:352 , HIS A:604 , ZN A:1638BINDING SITE FOR RESIDUE ZN A1639
3AC3SOFTWAREHIS B:242 , HIS B:244 , HIS B:329 , ASP B:352 , ZN B:1639BINDING SITE FOR RESIDUE ZN B1638
4AC4SOFTWAREASP B:246 , HIS B:247 , ASP B:352 , HIS B:604 , ZN B:1638BINDING SITE FOR RESIDUE ZN B1639

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XR1)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:230 -Pro A:231
2Thr A:507 -Ser A:508
3Gln A:594 -Pro A:595
4Phe B:230 -Pro B:231
5Thr B:507 -Ser B:508
6Gln B:594 -Pro B:595

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XR1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XR1)

(-) Exons   (0, 0)

(no "Exon" information available for 2XR1)

(-) 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:605
 aligned with Q8PZ03_METMA | Q8PZ03 from UniProtKB/TrEMBL  Length:637

    Alignment length:635
                                    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       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632     
         Q8PZ03_METMA     3 IEDVLLDLKHKIEKNLPAGVTITDVEFEGPQLVLYTEEPRKFADDGNIIRNLAKELRTRIAMRPDPRVLATPEDSISIIEEVVPKESVISSYYFDPDSGEVIIEAEKPGLVIGKHGATLREITKQIGWIPKVVRTPPIKSRTVKNIREFMRNNLKERKEILKTVGRKIHRECTSKDQWVRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVGSDENMTPYLYVPEVFPLNQIDAVIVTHAHLDHQGLVPLLFKYGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYESGMVAKTLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYEKTRLFDPAVNKFPRVETVISEATYGNANAFQPALKDAEKHLQMVVKNTIERGGIAVIPAFAVGRSQEVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHATHPEYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPCVILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGYQADGTIGRRIQKGWKEIPMTGKNGSTEMLKMNMEVQVVDGFSGHSDRRQLMEYVKRMQPRPERVFTEHGDEKACVDLASSVYKKLKIETRALTNLETVRLL 637
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh........eeee..eeeeee.hhhhhhhhhhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhhhhhhh.eeeeee.....eeeeee.hhhhhhh..hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee........eeeee....eeee......................hhhhh.eee....hhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhheee......eeee..eeeeeee.......eeeeeee....eeeee.......................eeeee...........hhhhhhhhhhhhh--------.eeee....hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhhhhhh------......eeee.-hhhhhhh----...eeee.......hhhhhhhhhhh.....eeee.......hhhhhhhh....-----------......eeee........hhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhh.eeee.....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xr1 A   3 IEDVLLDLKHKIEKNLPAGVTITDVEFEGPQLVLYTEEPRKFADDGNIIRNLAKELRTRIAMRPDPRVLATPEDSISIIEEVVPKESVISSYYFDPDSGEVIIEAEKPGLVIGKHGATLREITKQIGWIPKVVRTPPIKSRTVKNIREFMRNNLKERKEILKTVGRKIHRECTSKDQWVRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVGSDENMTPYLYVPEVFPLNQIDAVIVTHAHLDHQGLVPLLFKYGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYESGMVAKTLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYEKTRLFDPAVNKFPRVETVISEATYGNANAFQPALKDAEKHLQMVV--------IAVIPAFAVGRSQEVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHATHPEYLNNDLRKLI------PFLSECFKPVD-HEARQKI----QPCVILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGYQADGTIGRRIQKGWKE-----------MLKMNMEVQVVDGFSGHSDRRQLMEYVKRMQPRPERVFTEHGDEKACVDLASSVYKKLKIETRALTNLETVRLL 637
                                    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       262       272       282       292       302       312       322       332       342       352       362       372       382       392        |-       412       422       432       442       452       462       | -    |  482    | |492  |    502       512       522       532       542       552         - |     572       582       592       602       612       622       632     
                                                                                                                                                                                                                                                                                                                                                                                                                                        401      410                                                         470    477       487 |   495  500                                                 552         564                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                489                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:611
 aligned with Q8PZ03_METMA | Q8PZ03 from UniProtKB/TrEMBL  Length:637

    Alignment length:637
                                    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       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       
         Q8PZ03_METMA     1 MPIEDVLLDLKHKIEKNLPAGVTITDVEFEGPQLVLYTEEPRKFADDGNIIRNLAKELRTRIAMRPDPRVLATPEDSISIIEEVVPKESVISSYYFDPDSGEVIIEAEKPGLVIGKHGATLREITKQIGWIPKVVRTPPIKSRTVKNIREFMRNNLKERKEILKTVGRKIHRECTSKDQWVRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVGSDENMTPYLYVPEVFPLNQIDAVIVTHAHLDHQGLVPLLFKYGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYESGMVAKTLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYEKTRLFDPAVNKFPRVETVISEATYGNANAFQPALKDAEKHLQMVVKNTIERGGIAVIPAFAVGRSQEVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHATHPEYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPCVILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGYQADGTIGRRIQKGWKEIPMTGKNGSTEMLKMNMEVQVVDGFSGHSDRRQLMEYVKRMQPRPERVFTEHGDEKACVDLASSVYKKLKIETRALTNLETVRLL 637
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------     ---KH_2-2xr1   B01 B:77-  164                                                              ------------------------Lactamase_B-2xr1B03 B:189-452                                                                                                                                                                                                                                           ------------------     --------------------------------------------------------------------------------        RMMBL-2xr1B05 B:564-608                      ----------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------     ---KH_2-2xr1   B02 B:77-  164                                                              ------------------------Lactamase_B-2xr1B04 B:189-452                                                                                                                                                                                                                                           ------------------     --------------------------------------------------------------------------------        RMMBL-2xr1B06 B:564-608                      ----------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------     ------------   ---------  ---------------   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Beta-Casp-2xr1B07 B:421-546                                                                                                   ---------        -------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------     ------------   ---------  ---------------   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Beta-Casp-2xr1B08 B:421-546                                                                                                   ---------        -------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhh..........eeee..eeeeee.hhhhhhhhhhhhhhhhhhhh..eeeee..-----hhhhhhhhhhhh---..eeeeee.--..eeeeee.hhhhhh---hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee........eeeee....eeee......................hhhhh.eee....hhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhheee......eeee..eeeeeee.......eeeeeee....eeeee.......................eeeee...........hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhhh-----hhhhh..eeee.hhhhhhhhhhh....eeee.......hhhhhhhhhhh.....eeee.......hhhhhhhh...ee..--------.ee...eeee........hhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhh.eeee.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xr1 B   1 MPIEDVLLDLKHKIEKNLPAGVTITDVEFEGPQLVLYTEEPRKFADDGNIIRNLAKELRTRIAMRPDP-----PEDSISIIEEVV---SVISSYYFD--SGEVIIEAEKPGLVI---GATLREITKQIGWIPKVVRTPPIKSRTVKNIREFMRNNLKERKEILKTVGRKIHRECTSKDQWVRVTALGGCKEVGRSCFLLSTPESRILIDCGVNVGSDENMTPYLYVPEVFPLNQIDAVIVTHAHLDHQGLVPLLFKYGYEGPVYCTPPTRDLMVLLQLDYIDVAAKEGKKIPYESGMVAKTLKHTIPLDYEEVTDIAPDIKLTFHNAGHILGSAISHFHIGDGLHNVVFTGDYKYEKTRLFDPAVNKFPRVETVISEATYGNANAFQPALKDAEKHLQMVVKNTIERGGIAVIPAFAVGRSQEVMIVLEESIRKGLIPEVPVYLDGMIWEATAIHATHPEYLNNDLRKLI-----NPFLSECFKPVDSHEARQKIIQNPQPCVILATSGMMNGGPVMEYFKAFAEDPRNTLVFVGYQADGTIGRRIQKGWKEIPM--------MLKMNMEVQVVDGFSGHSDRRQLMEYVKRMQPRPERVFTEHGDEKACVDLASSVYKKLKIETRALTNLETVRLL 637
                                    10        20        30        40        50        60       | -   |    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       450       460       470     | 480       490       500       510       520       530       540       550    |    -   |   570       580       590       600       610       620       630       
                                                                                              68    74         85  89      97  |           114 118                                                                                                                                                                                                                                                                                                                                                             470   476                                                                            555      564                                                                         
                                                                                                                             100
   Legend:   → Mismatch (orange background)
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  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 2XR1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XR1)

(-) Pfam Domains  (4, 8)

Asymmetric Unit
(-)
Clan: KH (43)
(-)
Clan: Metallo-HOrase (67)
(-)
Clan: RMMBL_DRMBL (2)
(-)
Clan: no clan defined [family: Beta-Casp] (2)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8PZ03_METMA | Q8PZ03)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.

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  2xr1
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 Related Entries

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