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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACTIVE SITE MUTANT OF METHANOBACTERIUM THERMOAUTOTROPHICUM NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
 
Authors :  V. Saridakis, D. Christendat, M. S. Kimber, A. M. Edwards, E. F. Pai
Date :  18 Jan 01  (Deposition) - 14 Mar 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Dinucleotide Binding Fold, Active Site Mutant, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Saridakis, D. Christendat, M. S. Kimber, A. Dharamsi, A. M. Edwards E. F. Pai
Insights Into Ligand Binding And Catalysis Of A Central Ste In Nad+ Synthesis: Structures Of Methanobacterium Thermoautotrophicum Nmn Adenylyltransferase Complexes.
J. Biol. Chem. V. 276 7225 2001
PubMed-ID: 11063748  |  Reference-DOI: 10.1074/JBC.M008810200

(-) Compounds

Molecule 1 - NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
    ChainsA
    EC Number2.7.7.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificMETHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid145262

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (6x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NMN1Ligand/IonBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1NMN6Ligand/IonBETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
2SO46Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:11 , ARG A:47 , GLY A:132 , THR A:133 , ARG A:136 , HOH A:2000BINDING SITE FOR RESIDUE SO4 A 1759
2AC2SOFTWAREVAL A:9 , GLY A:10 , ARG A:11 , GLY A:38 , SER A:39 , ASP A:80 , ILE A:81 , ASN A:84 , TRP A:87 , ASN A:105 , LEU A:107 , HOH A:2018 , HOH A:2020BINDING SITE FOR RESIDUE NMN A 1340

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HYB)

(-) Exons   (0, 0)

(no "Exon" information available for 1HYB)

(-) 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:161
 aligned with NADM_METTH | O26253 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
           NADM_METTH     1 MRGLLVGRMQPFHRGHLQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPPLFYRDRYSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLA 167
               SCOP domains d1hyba_ A: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                        SCOP domains
               CATH domains 1hybA00 A:4-170 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh.eeeeee.............hhhhhhhhhhhhhhhh..hhh.eeeee.....hhhhhhhhhhhhh....eee..hhhhhhhhhhh..eee...------.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hyb A   4 MRGLLVGRMQPFHRGALQVIKSILEEVDELIICIGSAQLSHSIRDPFTAGERVMMLTKALSENGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDRVYSGNPLVQRLFSEDGYEVTAPP------YSGTEVRRRMLDDGDWRSLLPESVVEVIDEINGVERIKHLA 170
                                    13        23        33        43        53        63        73        83        93       103       113       123      |133       143       153       163       
                                                                                                                                                 123    130                                        

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HYB)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (NADM_METTH | O26253)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000309    nicotinamide-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009435    NAD biosynthetic process    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019363    pyridine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NADM_METTH | O262531ej2 1m8f 1m8g 1m8j 1m8k 4yp5 4yp6 4yp7

(-) Related Entries Specified in the PDB File

1ej2 1EJ2 IS THE CRYSTAL STRUCTURE OF METHANOBACTERIUM THERMOAUTOTROPHICUM NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE