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(-) Description

Title :  RNASE P PROTEIN FROM THERMOTOGA MARITIMA
 
Authors :  A. V. Kazantsev, A. A. Krivenko, D. J. Harrington, R. J. Carter, S. R. Holbrook, P. D. Adams, N. R. Pace, Berkeley Structural Genomics Center (Bsgc)
Date :  14 Feb 03  (Deposition) - 24 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 6:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 7:  A,C  (1x)
Biol. Unit 8:  B,D  (1x)
Biol. Unit 9:  B (1x),D (1x)
Biol. Unit 10:  A (1x),C (1x)
Biol. Unit 11:  B (1x),D (1x)
Biol. Unit 12:  B (1x),C (1x),D (1x)
Biol. Unit 13:  B (1x),C (1x),D (1x)
Keywords :  Endonuclease, Rnase, Alfa-Beta Sandwich, Dimer, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. V. Kazantsev, A. A. Krivenko, D. J. Harrington, R. J. Carter, S. R. Holbrook, P. D. Adams, N. R. Pace
High-Resolution Structure Of Rnase P Protein From Thermotoga Maritima.
Proc. Natl. Acad. Sci. Usa V. 100 7497 2003
PubMed-ID: 12799461  |  Reference-DOI: 10.1073/PNAS.0932597100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE P PROTEIN COMPONENT
    Chains: A, C, B, D
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4TA
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNPA OR TM1463
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RNASEP PROTEIN, RNASE P PROTEIN, PROTEIN C5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):   C 
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 6 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 7 (1x): A C 
Biological Unit 8 (1x):  B D
Biological Unit 9 (1x):  B (1x) D (1x)
Biological Unit 10 (1x): A (1x) C (1x) 
Biological Unit 11 (1x):  B (1x) D (1x)
Biological Unit 12 (1x):  B (1x)C (1x)D (1x)
Biological Unit 13 (1x):  B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2SO416Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION
Biological Unit 5 (2, 7)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1MSE-1Mod. Amino AcidSELENOMETHIONINE
2SO4-1Ligand/IonSULFATE ION
Biological Unit 7 (2, 7)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION
Biological Unit 8 (2, 13)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO411Ligand/IonSULFATE ION
Biological Unit 9 (2, 7)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 10 (2, 4)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 11 (2, 7)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 12 (2, 7)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 13 (2, 7)
No.NameCountTypeFull Name
1MSE1Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR D:58 , ARG D:59 , LYS D:62 , PHE D:96 , HOH D:7274BINDING SITE FOR RESIDUE SO4 D 5001
02AC2SOFTWAREARG B:89 , LYS B:90 , HOH B:7200 , HOH B:7229 , HOH B:7303 , HOH B:7488BINDING SITE FOR RESIDUE SO4 B 5002
03AC3SOFTWAREARG C:89 , LYS C:90 , HOH C:7059 , HOH C:7294BINDING SITE FOR RESIDUE SO4 C 5003
04AC4SOFTWAREARG A:89 , LYS A:90 , HOH A:7065 , HOH A:7325 , HOH A:7457 , HOH A:7542BINDING SITE FOR RESIDUE SO4 A 5004
05AC5SOFTWAREARG C:65 , TRP C:66 , HOH C:7230 , HOH C:7392BINDING SITE FOR RESIDUE SO4 C 5005
06AC6SOFTWAREARG B:65 , TRP B:66 , HOH B:7039 , HOH B:7255 , HOH B:7321 , HOH B:7552 , ARG D:73 , HOH D:7245BINDING SITE FOR RESIDUE SO4 B 5006
07AC7SOFTWARETRP B:102 , ARG B:105 , ARG D:65 , TRP D:66 , HOH D:7086BINDING SITE FOR RESIDUE SO4 D 5007
08AC8SOFTWAREARG B:60 , LYS B:64 , HOH B:7045 , HOH B:7056 , HOH B:7348 , LYS D:22BINDING SITE FOR RESIDUE SO4 B 5008
09AC9SOFTWAREARG A:52 , ARG A:60 , HOH A:7030 , LYS C:22BINDING SITE FOR RESIDUE SO4 A 5009
10BC1SOFTWARELYS A:22 , ARG C:60 , LYS C:64 , HOH C:7089 , HOH C:7105 , HOH C:7149BINDING SITE FOR RESIDUE SO4 C 5010
11BC2SOFTWAREARG B:52 , LYS B:56 , ALA B:57 , ARG B:60 , HOH B:7296 , HOH B:7490BINDING SITE FOR RESIDUE SO4 B 5011
12BC3SOFTWAREARG B:72 , ARG B:73BINDING SITE FOR RESIDUE SO4 B 5012
13BC4SOFTWAREGLU B:30 , ARG B:89 , HOH B:7306BINDING SITE FOR RESIDUE SO4 B 5013
14BC5SOFTWAREARG D:89 , LYS D:90 , HOH D:7093 , HOH D:7224 , HOH D:7270 , HOH D:7313BINDING SITE FOR RESIDUE SO4 D 5014
15BC6SOFTWAREARG D:15 , ARG D:37 , HOH D:7235 , HOH D:7401BINDING SITE FOR RESIDUE SO4 D 5015
16BC7SOFTWAREARG D:12 , LEU D:13 , ARG D:14 , HOH D:7519BINDING SITE FOR RESIDUE SO4 D 5016

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NZ0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:116 -Gly A:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NZ0)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  4A:54-68
B:54-68
C:54-68
D:54-68
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  1A:54-68
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  1-
-
C:54-68
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  1-
B:54-68
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  1-
-
-
D:54-68
Biological Unit 5 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  4A:54-68
B:54-68
C:54-68
D:54-68
Biological Unit 6 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  4A:54-68
B:54-68
C:54-68
D:54-68
Biological Unit 7 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  2A:54-68
-
C:54-68
-
Biological Unit 8 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  2-
B:54-68
-
D:54-68
Biological Unit 9 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  2-
B:54-68
-
D:54-68
Biological Unit 10 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  2A:54-68
-
C:54-68
-
Biological Unit 11 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  2-
B:54-68
-
D:54-68
Biological Unit 12 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  3-
B:54-68
C:54-68
D:54-68
Biological Unit 13 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBONUCLEASE_PPS00648 Bacterial ribonuclease P protein component signature.RNPA_THEMA54-68
 
 
 		  3-
B:54-68
C:54-68
D:54-68

(-) Exons   (0, 0)

(no "Exon" information available for 1NZ0)

(-) 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:109
 aligned with RNPA_THEMA | Q9X1H4 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:109
                                    18        28        38        48        58        68        78        88        98       108         
           RNPA_THEMA     9 ERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
               SCOP domains d1nz0a_ A: RNase P protein                                                                                    SCOP domains
               CATH domains 1nz0A00 A:9-117  [code=3.30.230.10, no name defined]                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhheeee...eeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------RIBONUCLEASE_P ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1nz0 A   9 ERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGmDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
                                    18        28        38  |     48        58        68        78        88        98       108         
                                                           41-MSE                                                                        


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with RNPA_THEMA | Q9X1H4 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:110
                                    17        27        37        47        57        67        77        87        97       107       117
           RNPA_THEMA     8 RERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
               SCOP domains d1nz0b_ B: RNase P protein                                                                                     SCOP domains
               CATH domains 1nz0B00 B:8-117  [code=3.30.230.10, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhheeee...eeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhh...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------RIBONUCLEASE_P ------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1nz0 B   8 RERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGmDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
                                    17        27        37   |    47        57        67        77        87        97       107       117
                                                            41-MSE                                                                        


Chain C from PDB  Type:PROTEIN  Length:107
 aligned with RNPA_THEMA | Q9X1H4 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:107
                                    20        30        40        50        60        70        80        90       100       110       
           RNPA_THEMA    11 LRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
               SCOP domains d1nz0c_ C: RNase P protein                                                                                  SCOP domains
               CATH domains 1nz0C00 C:11-117  [code=3.30.230.10, no name defined]                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhheeee...eeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------RIBONUCLEASE_P ------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1nz0 C  11 LRLRRDFLLIFKEGKSLQNEYFVVLFRKNGmDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
                                    20        30        40|       50        60        70        80        90       100       110       
                                                         41-MSE                                                                        


Chain D from PDB  Type:PROTEIN  Length:111
 aligned with RNPA_THEMA | Q9X1H4 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:111
                                    16        26        36        46        56        66        76        86        96       106       116 
           RNPA_THEMA     7 RRERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGLDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
               SCOP domains d1nz0d_ D: RNase P protein                                                                                      SCOP domains
               CATH domains 1nz0D00 D:7-117  [code=3.30.230.10, no name defined]                                                            CATH domains
           Pfam domains (1) Ribonuclease_P-1nz0D01 D:7-116                                                                                - Pfam domains (1)
           Pfam domains (2) Ribonuclease_P-1nz0D02 D:7-116                                                                                - Pfam domains (2)
           Pfam domains (3) Ribonuclease_P-1nz0D03 D:7-116                                                                                - Pfam domains (3)
           Pfam domains (4) Ribonuclease_P-1nz0D04 D:7-116                                                                                - Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhheeee...eeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------RIBONUCLEASE_P ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1nz0 D   7 RRERLRLRRDFLLIFKEGKSLQNEYFVVLFRKNGmDYSRLGIVVKRKFGKATRRNKLKRWVREIFRRNKGVIPKGFDIVVIPRKKLSEEFERVDFWTVREKLLNLLKRIEG 117
                                    16        26        36    |   46        56        66        76        86        96       106       116 
                                                             41-MSE
   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  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RNPA_THEMA | Q9X1H4)
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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer 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.

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