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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHEAL RNASE P PROTEIN PH1481P IN COMPLEX WITH PH1877P
 
Authors :  S. Kawano, Y. Kakuta, T. Nakashima, I. Tanaka, M. Kimura
Date :  19 Jul 05  (Deposition) - 27 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ribonuclease, Rna Binding Protein, Rna Recognition Motif, Protein-Protein Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kawano, T. Nakashima, Y. Kakuta, I. Tanaka, M. Kimura
Crystal Structure Of Protein Ph1481P In Complex With Protein Ph1877P Of Archaeal Rnase P From Pyrococcus Horikoshii Ot3: Implication Of Dimer Formation Of The Holoenzyme
J. Mol. Biol. V. 357 583 2006
PubMed-ID: 16430919  |  Reference-DOI: 10.1016/J.JMB.2005.12.086
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE P PROTEIN COMPONENT 3
    Chains: A, B
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21 CONDONPLUS (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH1877
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: RNASE P COMPONENT 3
 
Molecule 2 - RIBONUCLEASE P PROTEIN COMPONENT 2
    Chains: C, D
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21 CODONPLUS (DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH1481
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: RNASE P COMPONENT 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1ACY16Ligand/IonACETIC ACID
2BOG2Ligand/IonB-OCTYLGLUCOSIDE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:154 , GLY A:189 , HOH A:2047 , HOH A:2052 , LEU C:46 , TYR C:76 , TYR C:79 , TYR D:76BINDING SITE FOR RESIDUE BOG A 1001
02AC2SOFTWAREHOH B:2031 , THR C:49 , GLY C:50 , LEU D:46 , TYR D:76 , TYR D:79BINDING SITE FOR RESIDUE BOG D 1002
03AC3SOFTWAREGLU A:82 , SER A:102 , SER A:130 , PRO A:133 , HOH A:2037BINDING SITE FOR RESIDUE ACY A 2001
04AC4SOFTWAREARG A:179 , LYS A:196 , GLU C:33 , ASN C:91 , HOH C:2050BINDING SITE FOR RESIDUE ACY A 2002
05AC5SOFTWAREARG B:15 , GLU B:82 , SER B:130 , ARG B:132 , PRO B:133 , HOH B:2025 , HOH B:2043BINDING SITE FOR RESIDUE ACY B 2003
06AC6SOFTWAREILE B:34 , LYS B:44 , TYR B:52BINDING SITE FOR RESIDUE ACY B 2004
07AC7SOFTWAREASP B:16 , GLU B:18 , GLU B:171 , HOH B:2052BINDING SITE FOR RESIDUE ACY B 2005
08AC8SOFTWAREHOH B:2015 , HOH B:2065 , HOH D:1050BINDING SITE FOR RESIDUE ACY B 2006
09AC9SOFTWARETHR C:105 , ILE C:106 , LYS C:107BINDING SITE FOR RESIDUE ACY C 2007
10BC1SOFTWAREASP C:26 , ACY C:2010BINDING SITE FOR RESIDUE ACY C 2008
11BC2SOFTWARESER C:25 , ASP C:26 , ACY C:2012BINDING SITE FOR RESIDUE ACY C 2009
12BC3SOFTWAREASP C:26 , GLY C:27 , ASP C:28 , ACY C:2008BINDING SITE FOR RESIDUE ACY C 2010
13BC4SOFTWARELYS A:172 , TRP A:173 , ASP C:26 , ACY C:2012BINDING SITE FOR RESIDUE ACY A 2011
14BC5SOFTWAREACY A:2011 , ILE C:24 , SER C:25 , LYS C:66 , ACY C:2009 , HOH C:2049BINDING SITE FOR RESIDUE ACY C 2012
15BC6SOFTWAREHOH A:2066 , LYS C:112 , PHE C:113 , LYS C:116 , HOH C:2078 , HOH C:2082BINDING SITE FOR RESIDUE ACY A 2013
16BC7SOFTWAREPHE C:90 , ASN C:91 , LYS C:112 , PHE C:113 , HOH C:2022 , HOH C:2025BINDING SITE FOR RESIDUE ACY C 2014
17BC8SOFTWAREGLU A:171 , TRP A:173 , ARG C:94 , HOH C:2023BINDING SITE FOR RESIDUE ACY C 2015
18BC9SOFTWAREPRO B:139 , GLU C:44 , HOH C:2046BINDING SITE FOR RESIDUE ACY C 2016

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CZV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2CZV)

(-) 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:208
 aligned with RNP3_PYRHO | O59543 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        
           RNP3_PYRHO     2 VGGGGVKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILKR 209
               SCOP domains d2czva_ A: Ribonuclease P protein component 3, Rnp3                                                                                                                                                              SCOP domains
               CATH domains 2czvA00 A:2-209 Metal-dependent hydrolases                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.hhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eee...........hhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhh.hhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czv A   2 VGGGGVKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILKR 209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with RNP3_PYRHO | O59543 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:206
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      
           RNP3_PYRHO     6 GVKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILKRLK 211
               SCOP domains d2czvb_ B: Ribonuclease P protein component 3, Rnp3                                                                                                                                                            SCOP domains
               CATH domains 2czvB00 B:6-211 Metal-dependent hydrolases                                                                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eee...........hhhhhhhhhhh..eeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh.hhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2czv B   6 GVKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILKRLK 211
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205      


Chain C from PDB  Type:PROTEIN  Length:118
 aligned with RNP2_PYRHO | O59150 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           RNP2_PYRHO     3 RKLKTLPPTLRDKNRYIAFEIISDGDFTKDEVKELIWKSSLEVLGETGTAIVKPWLIKFDPNTKTGIVRCDREYVEYLRFALMLVSEFNGKRLIIRTLGVSGTIKRLKRKFLAKYGWK 120
               SCOP domains d2czvc1 C:3-120 RNase P protein component 2, Rnp2                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..ee.eeeeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2czv C   3 RKLKTLPPTLRDKNRYIAFEIISDGDFTKDEVKELIWKSSLEVLGETGTAIVKPWLIKFDPNTKTGIVRSDREYVEYLRFALMLVSEFNGKRLIIRTLGVSGTIKRLKRKFLAKYGWK 120
                                    12        22        32        42        52        62        72        82        92       102       112        


Chain D from PDB  Type:PROTEIN  Length:119
 aligned with RNP2_PYRHO | O59150 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:119
                                    11        21        31        41        51        61        71        81        91       101       111         
           RNP2_PYRHO     2 MRKLKTLPPTLRDKNRYIAFEIISDGDFTKDEVKELIWKSSLEVLGETGTAIVKPWLIKFDPNTKTGIVRCDREYVEYLRFALMLVSEFNGKRLIIRTLGVSGTIKRLKRKFLAKYGWK 120
               SCOP domains d2czvd_ D: RNase P protein component 2, Rnp2                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..eeeeeeeeeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2czv D   2 MRKLKTLPPTLRDKNRYIAFEIISDGDFTKDEVKELIWKSSLEVLGETGTAIVKPWLIKFDPNTKTGIVRSDREYVEYLRFALMLVSEFNGKRLIIRTLGVSGTIKRLKRKFLAKYGWK 120
                                    11        21        31        41        51        61        71        81        91       101       111
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CZV)

(-) Gene Ontology  (14, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNP3_PYRHO | O59543)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0004526    ribonuclease P activity    Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0001682    tRNA 5'-leader removal    Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030677    ribonuclease P complex    A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs.

Chain C,D   (RNP2_PYRHO | O59150)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0004526    ribonuclease P activity    Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0001682    tRNA 5'-leader removal    Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030677    ribonuclease P complex    A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs.

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  2czv
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  RNP3_PYRHO | O59543
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 Related Entries

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

UniProtKB/Swiss-Prot
        RNP3_PYRHO | O59543: 1v77

(-) Related Entries Specified in the PDB File

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