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(-) Description

Title :  CRYSTAL STRUCTURE OF NUDIX FAMILY PROTEIN WITH NAD
 
Authors :  D. Zhang, Z. Guan, T. Zou, P. Yin
Date :  15 Mar 16  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Nudix Family, Complex, Nad, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Zhang, Y. Liu, Q. Wang, Z. Guan, J. Wang, J. Liu, T. Zou, P. Yin
Structural Basis Of Prokaryotic Nad-Rna Decapping By Nudc
Cell Res. V. 26 1062 2016
PubMed-ID: 27561816  |  Reference-DOI: 10.1038/CR.2016.98

(-) Compounds

Molecule 1 - NADH PYROPHOSPHATASE
    Chains: A, C
    EC Number: 3.6.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NUDC, YJAD, B3996, JW5548
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: N6-ADENOSINE-METHYLTRANSFERASE 70 KDA SUBUNIT, N6-ADENOSINE- METHYLTRANSFERASE SUBUNIT METTL14

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:98 , CYS A:101 , CYS A:116 , CYS A:119binding site for residue ZN A 301
2AC2SOFTWARECYS A:130 , ILE A:132 , PHE A:160 , GLN A:192 , TRP A:194 , PHE A:196 , SER A:199 , MET A:201 , THR A:239 , VAL A:240 , ALA A:241 , HOH A:413 , HOH A:474 , GLU C:111 , TYR C:124binding site for residue NAD A 302
3AC3SOFTWARECYS C:98 , CYS C:101 , CYS C:116 , CYS C:119binding site for residue ZN C 301
4AC4SOFTWAREGLU A:111 , TYR A:124 , ALA C:128 , CYS C:130 , PHE C:160 , TRP C:194 , PHE C:196 , SER C:199 , MET C:201 , VAL C:240 , ALA C:241 , HOH C:470binding site for residue NAD C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:196 -Pro A:197
2Phe C:196 -Pro C:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ISY)

(-) 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeeeeee..eee.hhhh..eee.hhhh....eeeeeeee..eeeeeee......eehhhhhh..hhhhhhhhhhhhhhhhhhhh..........eee......eee.....ee....eeeeeeeeee..eeeeeee..........eeee.....hhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeee...........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5isy A   2 DRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEQSGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAMCEY 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251|| 
                                                                                                                                                                                                                                                                                    252| 
                                                                                                                                                                                                                                                                                     255 


Chain C from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeeeeee..eee.hhhh..eee.hhhh....eeeeeeee..eeeeeee......eehhhhhh..hhhhhhhhhhhhhhhhhhhh...........ee......ee......ee....eeeeeeeeee..eeeeeee.......ee.eeee.....hhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeee...........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5isy C   2 DRIIEKDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEQSGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAM 251
                                 || 12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242         
                                 7|                                                                                                                                                                                                                                                  
                                  9
   Legend:   → Mismatch (orange background)
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  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 5ISY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        NUDC_ECOLI | P32664: 1vk6 2gb5

(-) Related Entries Specified in the PDB File

5is3