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(-) Description

Title :  CRYSTAL STRUCTURE OF PROTEIN PH1601P IN COMPLEX WITH PROTEIN PH1771P OF ARCHAEAL RIBONUCLEASE P FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  T. Honda, Y. Kakuta, M. Kimura
Date :  04 Oct 07  (Deposition) - 14 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribonuclease P Protein Subunits, Hetero Dimer, Hydrolase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Honda, Y. Kakuta, K. Kimura, J. Saho, M. Kimura
Structure Of An Archaeal Homolog Of The Human Protein Complex Rpp21-Rpp29 That Is A Key Core Component For The Assembly Of Active Ribonuclease P.
J. Mol. Biol. V. 384 652 2008
PubMed-ID: 18929577  |  Reference-DOI: 10.1016/J.JMB.2008.09.056

(-) Compounds

Molecule 1 - RIBONUCLEASE P PROTEIN COMPONENT 1
    Chains: A, C
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)CODONPLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNP1
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Strain: OT3
    Synonym: RNASE P COMPONENT 1
 
Molecule 2 - RIBONUCLEASE P PROTEIN COMPONENT 4
    Chains: B, D
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)CODONPLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNP4
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Strain: OT3
    Synonym: RNASE P COMPONENT 4

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NO39Ligand/IonNITRATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2NO34Ligand/IonNITRATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NO35Ligand/IonNITRATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS B:68 , CYS B:71 , CYS B:97 , CYS B:100BINDING SITE FOR RESIDUE ZN B 121
02AC2SOFTWARECYS D:68 , CYS D:71 , CYS D:97 , CYS D:100BINDING SITE FOR RESIDUE ZN D 121
03AC3SOFTWAREGLY A:25 , ARG A:26 , THR A:27 , TRP A:28 , HOH A:176 , TRP C:28BINDING SITE FOR RESIDUE NO3 A 128
04AC4SOFTWAREPRO B:77 , ARG D:82BINDING SITE FOR RESIDUE NO3 D 122
05AC5SOFTWAREARG C:54 , GLY C:65 , GLU C:67 , HOH C:161 , MET D:90 , PRO D:91 , HIS D:92 , HOH D:148BINDING SITE FOR RESIDUE NO3 D 123
06AC6SOFTWAREARG B:89 , GLN C:17 , SER C:19BINDING SITE FOR RESIDUE NO3 C 128
07AC7SOFTWAREHIS A:60 , ASP A:91 , VAL A:92BINDING SITE FOR RESIDUE NO3 A 130
08AC8SOFTWARETRP A:28 , GLY C:25 , ARG C:26 , THR C:27 , TRP C:28 , HOH C:160 , LYS D:88BINDING SITE FOR RESIDUE NO3 C 129
09AC9SOFTWARETHR C:74 , ARG C:75 , ARG C:115 , PRO C:116 , HOH C:155 , ARG D:43BINDING SITE FOR RESIDUE NO3 C 130
10BC1SOFTWAREPRO B:77 , GLY B:78 , ARG B:82 , VAL B:83 , ARG B:84 , ARG D:82 , THR D:96 , HOH D:192BINDING SITE FOR RESIDUE NO3 B 122
11BC2SOFTWARESER A:58 , THR A:59 , VAL A:92 , ILE A:94BINDING SITE FOR RESIDUE GOL A 131
12BC3SOFTWARETYR B:102 , ILE B:103 , PRO C:61BINDING SITE FOR RESIDUE GOL B 123
13BC4SOFTWARETYR D:102 , ILE D:103 , HOH D:171BINDING SITE FOR RESIDUE GOL D 124
14BC5SOFTWAREHIS A:60 , ALA A:62BINDING SITE FOR RESIDUE GOL A 132

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZAE)

(-) 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:105
 aligned with RNP1_PYRHO | O59425 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:105
                                    27        37        47        57        67        77        87        97       107       117     
           RNP1_PYRHO    18 GSYQEIIGRTWIFRGAHRGRVTRRNIIWHELIGLRVRIVGSTHPAFVGIEGYVIDETRNMLVIAGDRIWKVPKDVCIFEFEADDGTKIKIPGERLVGRPEMRLKK 122
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhh....................eeeeeee.hhhhh..eeeeeeee..eeeee...eeeee...eeeeee.....eeeee.hhhh..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2zae A  18 GSYQEIIGRTWIFRGAHRGRVTRRNIIWHELIGLRVRIVGSTHPAFVGIEGYVIDETRNMLVIAGDRIWKVPKDVSIFEFEADDGTKIKIPGERLVGRPEMRLKK 122
                                    27        37        47        57        67        77        87        97       107       117     


Chain B from PDB  Type:PROTEIN  Length:98
 aligned with RNP4_PYRHO | O59248 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:98
                                    20        30        40        50        60        70        80        90       100        
           RNP4_PYRHO    11 EKKEKKKIAIERIDTLFTLAERVARYSPDLAKRYVELALEIQKKAKVKIPRKWKRRYCKRCHTFLIPGVNARVRLRTKRMPHVVITCLECGYIMRYPY 108
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........................eeeeee.....eeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2zae B  11 EKKEKKKIAIERIDTLFTLAERVARYSPDLAKRYVELALEIQKKAKVKIPRKWKRRYCKRCHTFLIPGVNARVRLRTKRMPHVVITCLECGYIMRYPY 108
                                    20        30        40        50        60        70        80        90       100        


Chain C from PDB  Type:PROTEIN  Length:105
 aligned with RNP1_PYRHO | O59425 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:105
                                    26        36        46        56        66        76        86        96       106       116     
           RNP1_PYRHO    17 QGSYQEIIGRTWIFRGAHRGRVTRRNIIWHELIGLRVRIVGSTHPAFVGIEGYVIDETRNMLVIAGDRIWKVPKDVCIFEFEADDGTKIKIPGERLVGRPEMRLK 121
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------UPF0086-2zaeC01 C:37-121                                                              Pfam domains (1)
           Pfam domains (2) --------------------UPF0086-2zaeC02 C:37-121                                                              Pfam domains (2)
         Sec.struct. author hhhhhh...hhhhhh....................eeeeeee.hhhhh..eeeeeeee..eeeee...eeeee...eeeeee.....eeeee.hhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2zae C  17 QGSYQEIIGRTWIFRGAHRGRVTRRNIIWHELIGLRVRIVGSTHPAFVGIEGYVIDETRNMLVIAGDRIWKVPKDVSIFEFEADDGTKIKIPGERLVGRPEMRLK 121
                                    26        36        46        56        66        76        86        96       106       116     


Chain D from PDB  Type:PROTEIN  Length:98
 aligned with RNP4_PYRHO | O59248 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:98
                                    21        31        41        51        61        71        81        91       101        
           RNP4_PYRHO    12 KKEKKKIAIERIDTLFTLAERVARYSPDLAKRYVELALEIQKKAKVKIPRKWKRRYCKRCHTFLIPGVNARVRLRTKRMPHVVITCLECGYIMRYPYL 109
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------Rpr2-2zaeD01 D:21-102                                                             ------- Pfam domains (1)
           Pfam domains (2) ---------Rpr2-2zaeD02 D:21-102                                                             ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh........................eeeeee.....eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2zae D  12 KKEKKKIAIERIDTLFTLAERVARYSPDLAKRYVELALEIQKKAKVKIPRKWKRRYCKRCHTFLIPGVNARVRLRTKRMPHVVITCLECGYIMRYPYL 109
                                    21        31        41        51        61        71        81        91       101
   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 2ZAE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Rpr2] (3)
(-)
Clan: no clan defined [family: UPF0086] (5)

(-) Gene Ontology  (19, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (RNP1_PYRHO | O59425)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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: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:0006379    mRNA cleavage    Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    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:0000172    ribonuclease MRP complex    A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication.
    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 B,D   (RNP4_PYRHO | O59248)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RNP1_PYRHO | O59425: 1v76
        RNP4_PYRHO | O59248: 1x0t

(-) Related Entries Specified in the PDB File

1v76 1x0t