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(-) Description

Title :  CRYSTAL STRUCTURE OF MPY-RNASE J (MUTANT H84A), AN ARCHAEAL RNASE J FROM METHANOLOBUS PSYCHROPHILUS R15, COMPLEX WITH RNA
 
Authors :  D. F. Li, N. Feng
Date :  30 Dec 15  (Deposition) - 04 Jan 17  (Release) - 04 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Exoribonuclease, Beta-Casp, Mbl, Rnase J, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zheng, N. Feng, D. F. Li, J. Li, X. Z. Dong
Molecular Insights Into Catalysis And Processive Exonucleolytic Mechanisms Of Prokaryotic Rnase J Revealing Striking Parallels With That Of Eukaryotic Xrn1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEASE J
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-448
    Gene: RNJ, MPSY_0886
    Mutation: YES
    Organism Scientific: METHANOLOBUS PSYCHROPHILUS R15
    Organism Taxid: 1094980
    Synonym: RNASE J
 
Molecule 2 - RNA (5'-R(P*AP*AP*AP*AP*A)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:296 , SER A:297 , ARG A:298 , ARG A:299 , A C:5binding site for residue SO4 A 501
2AC2SOFTWAREASN A:213 , HOH A:614 , HOH B:608binding site for residue SO4 A 502
3AC3SOFTWARETYR A:366 , ARG B:36 , ARG B:39binding site for residue SO4 A 503
4AC4SOFTWAREHIS A:223 , MET A:224 , LYS A:227 , HOH A:607 , HOH A:668binding site for residue SO4 A 504
5AC5SOFTWAREARG A:36 , ARG A:39 , TYR B:366 , HOH B:631binding site for residue SO4 B 501
6AC6SOFTWAREARG B:271 , SER B:297 , ARG B:298 , A D:5binding site for residue SO4 B 502
7AC7SOFTWARELYS A:373 , GLY B:211 , ASN B:213 , ARG B:391binding site for residue SO4 B 503
8AC8SOFTWAREHIS B:223 , LYS B:227binding site for residue SO4 B 504
9AC9SOFTWAREHIS A:-15 , HIS A:-17 , GLY B:431 , HIS B:435binding site for residue SO4 B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HAB)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:60 -Ala A:61
2Gly B:60 -Ala B:61
3Phe B:122 -Gly B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HAB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HAB)

(-) Exons   (0, 0)

(no "Exon" information available for 5HAB)

(-) 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:456
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeeeee........eeeeee..eeeee.....hhhhhh.........hhhhhhhhh...hhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eee.....eeeee..eeeeeeee......eeeeeeee..eeeeee...............hhhhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.........eee.hhhhhhhhhhhhhh.hhh.eeeee........hhhhhhhh...........eeeee.....hhhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh..............eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hab A -19 SSHHHHHHSSGLVPASTEIGIIAVGGYNEMGRNMTAIRVNEDIIIIDMGIRLDRVQIHEDVDTDRMHSLELIEMGAIPDDTIMNEVNGNVRAIVCTHGALDHIGAIPKLAHRYAAPIIATPYTTALIKHQIDKNNIVALKAGETLEITKDITIEFINTQHSIIDTVFVAIHTPSGAVVYACDFKFDRTPTLGEVPDFDRLKELGKEGVIALITESTNAGRNGKTPSELIAHMMLKDVLLGTEESAVGMIVTTFASHIARVNSIVQFAQEMGRIPVLLGRSMERYVGTAYQLGYIDLPENVEIYGSRRDIDNALKKIMEAGKDKYLPVMTGHQGEPGAVLGRIANGETPFKVETGDRIIFSANVIPNPMTQANRYALETKLKMKGARIYDNVHVSGHAYREDHWELLRMLKPEHVIPAHGTIQMHSEYIQMAEDAGYSLGDTLHLLRNGEELYIEED 448
                                   -10   ||    5        15        25        35        45        55        65        75        85        95       105       115 ||    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      
                                        -6|                                                                                                                  117|                                                                                                                                                                                                                                                                                                                                   
                                          0                                                                                                                   125                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeee........eeeeee..eeeee.....hhhhhh.........hhhhhhhhh...hhhhhhhh..eeeeee....hhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh..........eee.....eee.....eeeeeee......eeeeeeee..eeeeee...............hhhhhhhhhhhheeeeeee...........hhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh.........eee.hhhhhhhhhhhhhh.hhh.eeeee........hhhhhhhh...........eeeee.....hhhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...............eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hab B -14 HHHSSGLVPRGSHMASTEIGIIAVGGYNEMGRNMTAIRVNEDIIIIDMGIRLDRVQIHEDVDTDRMHSLELIEMGAIPDDTIMNEVNGNVRAIVCTHGALDHIGAIPKLAHRYAAPIIATPYTTALIKHQIDSERKFGVKNNIVALKAGETLEITKDITIEFINTQHSIIDTVFVAIHTPSGAVVYACDFKFDRTPTLGEVPDFDRLKELGKEGVIALITESTNAGRNGKTPSELIAHMMLKDVLLGTEESAVGMIVTTFASHIARVNSIVQFAQEMGRIPVLLGRSMERYVGTAYQLGYIDLPENVEIYGSRRDIDNALKKIMEAGKDKYLPVMTGHQGEPGAVLGRIANGETPFKVETGDRIIFSANVIPNPMTQANRYALETKLKMKGARIYDNVHVSGHAYREDHWELLRMLKPEHVIPAHGTIQMHSEYIQMAEDAGYSLGDTLHLLRNGEELYIEED 448
                                    -5         5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445   


Chain C from PDB  Type:RNA  Length:5
                                     
                 5hab C   1 AAAAA   5


Chain D from PDB  Type:RNA  Length:5
                                     
                 5hab D   1 AAAAA   5
   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 5HAB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HAB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HAB)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

5haa