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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE J COMPLEXED WITH UMP
 
Authors :  M. Lu, H. Zhang, Q. Xu, Y. Hua, Y. Zhao
Date :  29 Jan 15  (Deposition) - 16 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribonuclease, Two-Metal-Ion, Dimerization, Manganese, Deinococcus Radiodurans, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, M. Lu, H. Zhang, J. Hu, C. Zhou, Q. Xu, A. M. U. H. Shah, H. Xu, L. Wang, Y. Hua
Structural Insights Into Catalysis And Dimerization Enhance Exonuclease Activity Of Rnase J
Nucleic Acids Res. V. 43 5550 2015
PubMed-ID: 25940620  |  Reference-DOI: 10.1093/NAR/GKV444

(-) Compounds

Molecule 1 - DR2417
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) ROSSETTA
    Expression System Taxid: 562
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN2Ligand/IonMANGANESE (II) ION
3U5P2Ligand/IonURIDINE-5'-MONOPHOSPHATE
4ZN4Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:84 , HIS A:86 , HIS A:153 , ASP A:175 , ZN A:602binding site for residue ZN A 601
02AC2SOFTWAREASP A:88 , HIS A:89 , ASP A:175 , HIS A:403 , ZN A:601binding site for residue ZN A 602
03AC3SOFTWAREGLY A:59 , ASP A:456binding site for residue MN A 603
04AC4SOFTWAREPRO A:371 , HOH A:764 , HOH A:779 , ARG B:407binding site for residue GOL A 604
05AC5SOFTWAREARG A:407 , HOH A:766 , VAL B:354 , TYR B:370 , HOH B:733binding site for residue GOL A 605
06AC6SOFTWARESER A:154 , SER A:247 , ILE A:347 , SER A:379 , GLY A:380 , HIS A:381 , HOH A:795binding site for residue U5P A 606
07AC7SOFTWAREASP B:88 , HIS B:89 , ASP B:175 , HIS B:403 , ZN B:602binding site for residue ZN B 601
08AC8SOFTWAREHIS B:84 , HIS B:86 , HIS B:153 , ASP B:175 , ZN B:601binding site for residue ZN B 602
09AC9SOFTWAREGLY B:59 , ASP B:456binding site for residue MN B 603
10AD1SOFTWAREHIS B:153 , SER B:154 , THR B:211 , ASN B:212 , ARG B:215 , SER B:379 , GLY B:380 , HIS B:381 , HOH B:753 , HOH B:793binding site for residue U5P B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XWT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:371 -Pro A:372
2His A:487 -Pro A:488
3Pro B:371 -Pro B:372
4His B:487 -Pro B:488

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XWT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XWT)

(-) Exons   (0, 0)

(no "Exon" information available for 4XWT)

(-) 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:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeee..eeeee...............eeee.hhhhhhh...eeeeee...hhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh....eeee.....eeee...eeeeeee........eeeeeee..eeeee..................hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..........hhhhhhhhhhh.eeeee........hhhhhhhh............eeee.......hhhhhhhhhhhhhhhh.eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......ee......eeeeee..eeeeeee....eeeee..ee...hhhhhhhhhhhhhhheeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xwt A  16 APTLEVIPLGGMGEIGKNITVFRYGDEIVVVDGGLAFPKAHQMGIDLIVPRIDYLLEHQDKIKGWILTHGHEDHIGGLPYIFARLPRVPVYGLPLTLALVREKLSEFGLQDVDLREVTYGDEVRFGQSFVAEFFCMTHSIPDNAGYILKTPVGDVLHTGDFKIDPDVGTGAGIVSDLERVEQAGKDGVLLLISDSTNAERPGHTPSEAEIARNLEEIIKGCRGRVFLTTFASQVYRIQNILDLAHRQGRRVVMEGRSMIKYAQAAQATGHMNPPEPFLTSEEVGELQDQQVLFVCTGSQGQPMAVLGRLAFGTHAKIALRRGDTVILSSNPIPGNEDAVNLIVNRLYEIGVDVVYPPTYRVHASGHASQEELATILNLTRPKFFLPWHGEPRHQINHAKLAQTLPRPPKRTLIAKNGDIVNLGPDEFRVSGTVAAGAVYVDGLGVGDVNDDVLLDRVNLSQEGLLILTAVLHPTPHVEVVARGFARPNRDLELQIRRVALEAVEQGLREKKRLEDVRDDMYGAVRRFTRKATGRNPVLIPMIV 558
                                    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       455       465       475       485       495       505       515       525       535       545       555   


Chain B from PDB  Type:PROTEIN  Length:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeee..eeeee...............eeee.hhhhhhh...eeeeee...hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhh......eee.....eeee...eeeeeee........eeeeeee..eeeee..................hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..........hhhhhhhhhhh.eeeee........hhhhhhhh............eeee.......hhhhhhhhhhhhhhhh.eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......ee......eeeee....eeeeee....eeeee..ee...hhhhhhhhhhhhhhheeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xwt B  16 APTLEVIPLGGMGEIGKNITVFRYGDEIVVVDGGLAFPKAHQMGIDLIVPRIDYLLEHQDKIKGWILTHGHEDHIGGLPYIFARLPRVPVYGLPLTLALVREKLSEFGLQDVDLREVTYGDEVRFGQSFVAEFFCMTHSIPDNAGYILKTPVGDVLHTGDFKIDPDVGTGAGIVSDLERVEQAGKDGVLLLISDSTNAERPGHTPSEAEIARNLEEIIKGCRGRVFLTTFASQVYRIQNILDLAHRQGRRVVMEGRSMIKYAQAAQATGHMNPPEPFLTSEEVGELQDQQVLFVCTGSQGQPMAVLGRLAFGTHAKIALRRGDTVILSSNPIPGNEDAVNLIVNRLYEIGVDVVYPPTYRVHASGHASQEELATILNLTRPKFFLPWHGEPRHQINHAKLAQTLPRPPKRTLIAKNGDIVNLGPDEFRVSGTVAAGAVYVDGLGVGDVNDDVLLDRVNLSQEGLLILTAVLHPTPHVEVVARGFARPNRDLELQIRRVALEAVEQGLREKKRLEDVRDDMYGAVRRFTRKATGRNPVLIPMIV 558
                                    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       455       465       475       485       495       505       515       525       535       545       555
   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 4XWT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XWT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XWT)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His A:487 - Pro A:488   [ RasMol ]  
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4xww