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(-) Description

Title :  CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM NMNAT IN COMPLEX WITH NADP
 
Authors :  R. Pfoh, D. Christendat, E. F. Pai, V. Saridakis
Date :  12 Mar 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Inhibitor, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pfoh, E. F. Pai, V. Saridakis
Nicotinamide Mononucleotide Adenylyltransferase Displays Alternate Binding Modes For Nicotinamide Nucleotides
Acta Crystallogr. , Sect. D V. 71 2032 2015
PubMed: search  |  Reference-DOI: 10.1107/S1399004715015497

(-) Compounds

Molecule 1 - NICOTINAMIDE-NUCLEOTIDE ADENYLYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.7.7.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 GOLD (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MTH_150
    Mutation: YES
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS (STRAIN ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H)
    Organism Taxid: 187420
    Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / DELTA H
    Synonym: NAD(+) DIPHOSPHORYLASE,NAD(+) PYROPHOSPHORYLASE,NMN ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NAP3Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NAP6Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , ARG A:11 , HIS A:16 , HIS A:19 , VAL A:22 , GLY A:38 , SER A:39 , ASP A:80 , ILE A:81 , ASN A:84 , TRP A:87 , ASN A:105 , LEU A:107 , PRO A:122 , LEU A:124 , PHE A:125 , TYR A:126 , SER A:131 , GLY A:132 , HOH A:2106 , HOH A:2115binding site for residue NAP A 2000
2AC2SOFTWAREGLY B:10 , ARG B:11 , HIS B:16 , HIS B:19 , VAL B:22 , GLY B:38 , SER B:39 , ASP B:80 , ILE B:81 , ASN B:84 , TRP B:87 , ASN B:105 , LEU B:124 , PHE B:125 , TYR B:126 , SER B:131 , GLY B:132 , HOH B:2103 , HOH B:2104 , HOH B:2112 , HOH B:2127 , HOH B:2131 , HOH B:2132 , HOH B:2134 , HOH B:2142binding site for residue NAP B 2000
3AC3SOFTWAREVAL C:9 , GLY C:10 , ARG C:11 , HIS C:16 , HIS C:19 , VAL C:22 , GLY C:38 , SER C:39 , ASP C:80 , ILE C:81 , ASN C:84 , TRP C:87 , ASN C:105 , LEU C:107 , LEU C:124 , PHE C:125 , TYR C:126 , SER C:131 , GLY C:132 , HOH C:2101 , HOH C:2105 , HOH C:2107 , HOH C:2119 , HOH C:2122 , HOH C:2137 , HOH C:2141 , HOH C:2143 , HOH C:2151 , HOH C:2155binding site for residue NAP C 2000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YP7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:13 -Pro A:14
2Gln B:13 -Pro B:14
3Gln C:13 -Pro C:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YP7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YP7)

(-) Exons   (0, 0)

(no "Exon" information available for 4YP7)

(-) 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:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eee........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yp7 A   3 TMRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIEDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLA 170
                                    12        22        32        42        52        62        72        82        92       102       112       122   ||  134       144       154       164      
                                                                                                                                                     126|                                         
                                                                                                                                                      129                                         


Chain B from PDB  Type:PROTEIN  Length:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eee......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yp7 B   3 TMRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIEDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLA 170
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        


Chain C from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eee......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yp7 C   3 TMRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIEDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHL 169
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
   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 4YP7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YP7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YP7)

(-) Gene Ontology  (10, 10)

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 Related Entries

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UniProtKB/Swiss-Prot
        NADM_METTH | O26253: 1ej2 1hyb 1m8f 1m8g 1m8j 1m8k 4yp5 4yp6

(-) Related Entries Specified in the PDB File

4yp5 4yp6