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(-) Description

Title :  STRUCTURE OF THE ARCHAEAL BETA-CASP PROTEIN WITH N-TERMINAL KH DOMAINS FROM METHANOTHERMOBACTER THERMAUTOTROPHICUS
 
Authors :  A. P. G. Silva, M. Chechik, R. T. Byrne, D. G. Waterman, C. L. Ng, E. J. Dods E. V. Koonin, A. A. Antson, C. Smits
Date :  13 Mar 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Beta-Casp, Rnase, Kh, Metallo-Beta-Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. G. Silva, M. Chechik, R. T. Byrne, D. G. Waterman, C. L. Ng, E. J. Dodson, E. V. Koonin, A. A. Antson, C. Smits
Structure And Activity Of A Novel Archaeal Beta-Casp Protein With N-Terminal Kh Domains.
Structure V. 19 622 2011
PubMed-ID: 21565697  |  Reference-DOI: 10.1016/J.STR.2011.03.002

(-) Compounds

Molecule 1 - CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector: PETYSBLIC-3C
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 187420
    Strain: DELTA H
    Synonym: BETA-CASP RNASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2PO44Ligand/IonPHOSPHATE ION
3ZN5Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:246 , HIS A:247 , ASP A:352 , HIS A:603 , ZN A:1638 , PO4 A:1639BINDING SITE FOR RESIDUE ZN A1637
02AC2SOFTWAREHIS A:242 , HIS A:244 , HIS A:329 , ASP A:352 , ZN A:1637 , PO4 A:1639BINDING SITE FOR RESIDUE ZN A1638
03AC3SOFTWAREHIS A:242 , HIS A:244 , ASP A:246 , HIS A:247 , HIS A:329 , ASP A:352 , HIS A:579 , HIS A:603 , ZN A:1637 , ZN A:1638BINDING SITE FOR RESIDUE PO4 A1639
04AC4SOFTWAREARG A:135 , ARG A:467 , ASP A:468 , HIS A:472 , PO4 A:1641 , ZN A:1642 , HIS B:472BINDING SITE FOR RESIDUE PO4 A1640
05AC5SOFTWARELYS A:464 , ARG A:467 , ASP A:468 , PO4 A:1640 , ZN A:1642 , HIS B:472BINDING SITE FOR RESIDUE PO4 A1641
06AC6SOFTWAREASP A:468 , HIS A:472 , PO4 A:1640 , PO4 A:1641 , HIS B:472BINDING SITE FOR RESIDUE ZN A1642
07AC7SOFTWARELEU A:225 , VAL A:227 , PHE A:230BINDING SITE FOR RESIDUE K A1643
08AC8SOFTWAREASP B:246 , HIS B:247 , ASP B:352 , HIS B:603 , ZN B:1638 , PO4 B:1639BINDING SITE FOR RESIDUE ZN B1637
09AC9SOFTWAREHIS B:242 , HIS B:244 , HIS B:329 , ASP B:352 , ZN B:1637 , PO4 B:1639BINDING SITE FOR RESIDUE ZN B1638
10BC1SOFTWAREHIS B:242 , HIS B:244 , ASP B:246 , HIS B:247 , HIS B:329 , ASP B:352 , HIS B:579 , HIS B:603 , ZN B:1637 , ZN B:1638BINDING SITE FOR RESIDUE PO4 B1639
11BC2SOFTWARELEU B:225 , VAL B:227 , PHE B:230BINDING SITE FOR RESIDUE K B1640

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:84 -Pro A:85
2Val B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YCB)

(-) 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:634
 aligned with O27271_METTH | O27271 from UniProtKB/TrEMBL  Length:636

    Alignment length:634
                                    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    
         O27271_METTH     3 SEMLEEIKRTIMQRLPERVQVAKVEFEGPEVVIYTKNPEIITENGNLIRDIAKDIRKRIIIRSDRSVLMDPEKAIRKIHEIVPEEAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWAPKILRTPPISSEIIERIRRTLRKNSKERKKILQQLGNRIHQKPKYDNDWARLTAMGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPYLYHYGYDGPVYCTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPDIRLTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVMESTYGGHEDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKGWKEIPLKDEDDKMRVYNVRMNIKTIEGFSGHSDRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRIETKTPLNLETVRIQ 636
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......eeeeeee..eeeeee..hhhhhh.hhhhhhhhhhhh..eeeee.hhhh.hhhhhhhhhhhh......eeeeeee....eeeeee..hhhhhh..hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee........eeeee....eeeeee.......hhhhhh..............eee....hhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhheee......eeee..eeeeeee.......eeeeeee......eee.......................eeeee....hhhhh..hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..eeee.hhhhhhhhhhh...eeee......hhhhhhhhhhhh.....eeee.......hhhhhhhh...eeeee.....eeeee...eeee........hhhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhh.eee......eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ycb A   3 SEMLEEIKRTIMQRLPERVQVAKVEFEGPEVVIYTKNPEIITENGNLIRDIAKDIRKRIIIRSDRSVLMDPEKAIRKIHEIVPEEAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWAPKILRTPPISSEIIERIRRTLRKNSKERKKILQQLGNRIHQKPKYDNDWARLTAMGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPYLYHYGYDGPVYCTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPDIRLTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVMESTYGGHEDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKGWKEIPLKDEDDKMRVYNVRMNIKTIEGFSGHSDRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRIETKTPLNLETVRIQ 636
                                    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    


Chain B from PDB  Type:PROTEIN  Length:635
 aligned with O27271_METTH | O27271 from UniProtKB/TrEMBL  Length:636

    Alignment length:635
                                    11        21        31        41        51        61        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       541       551       561       571       581       591       601       611       621       631     
         O27271_METTH     2 VSEMLEEIKRTIMQRLPERVQVAKVEFEGPEVVIYTKNPEIITENGNLIRDIAKDIRKRIIIRSDRSVLMDPEKAIRKIHEIVPEEAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWAPKILRTPPISSEIIERIRRTLRKNSKERKKILQQLGNRIHQKPKYDNDWARLTAMGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPYLYHYGYDGPVYCTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPDIRLTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVMESTYGGHEDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKGWKEIPLKDEDDKMRVYNVRMNIKTIEGFSGHSDRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRIETKTPLNLETVRIQ 636
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lactamase_B-2ycbB01 B:188-400                                                                                                                                                                                        --------------------Beta-Casp-2ycbB05 B:421-545                                                                                                  ----------------RMMBL-2ycbB03 B:562-606                      ------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Lactamase_B-2ycbB02 B:188-400                                                                                                                                                                                        --------------------Beta-Casp-2ycbB06 B:421-545                                                                                                  ----------------RMMBL-2ycbB04 B:562-606                      ------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhh.......eeeeeee..eeeeee..hhhhhh.hhhhhhhhhhhh.eeeeee.hhhh.hhhhhhhhhhhh......eeeeeee....eeeeee..hhhhhh..hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee........eeeee....eeeeee.......hhhhhh..............eee....hhhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhheee......eeee..eeeeeee.......eeeeeee......eee.......................eeeee....hhhhh..hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..eeee..hhhhhhhhh....eeee......hhhhhhhhhhhh.....eeee.......hhhhhhhh...eeee.......eeee...eeee........hhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh.eee......eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ycb B   2 VSEMLEEIKRTIMQRLPERVQVAKVEFEGPEVVIYTKNPEIITENGNLIRDIAKDIRKRIIIRSDRSVLMDPEKAIRKIHEIVPEEAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWAPKILRTPPISSEIIERIRRTLRKNSKERKKILQQLGNRIHQKPKYDNDWARLTAMGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPYLYHYGYDGPVYCTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPDIRLTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVMESTYGGHEDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKGWKEIPLKDEDDKMRVYNVRMNIKTIEGFSGHSDRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRIETKTPLNLETVRIQ 636
                                    11        21        31        41        51        61        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       541       551       561       571       581       591       601       611       621       631
   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 2YCB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O27271_METTH | O27271)
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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