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(-) Description

Title :  MOUSE NICOTINAMIDE N-METHYLTRANSFERASE
 
Authors :  J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Date :  27 Aug 06  (Deposition) - 12 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Nicotinamide N-Methyltransferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, J. Min, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Mouse Nicotinamide N-Methyltransferase In Complex With Sah
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICOTINAMIDE N-METHYLTRANSFERASE
    ChainsA, B, C, D
    EC Number2.1.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneNNMT
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:12 , TYR A:21 , TYR A:26 , GLY A:64 , SER A:65 , GLY A:66 , THR A:68 , TYR A:70 , ASP A:86 , TYR A:87 , THR A:88 , ASN A:91 , CYS A:142 , ASP A:143 , VAL A:144 , THR A:164 , LEU A:165 , ALA A:170 , HOH A:4014 , HOH A:4070 , HOH A:4075BINDING SITE FOR RESIDUE SAH A 4001
2AC2SOFTWARETYR B:12 , TYR B:21 , TYR B:26 , GLY B:64 , SER B:65 , GLY B:66 , THR B:68 , TYR B:70 , ASP B:86 , TYR B:87 , THR B:88 , ASN B:91 , ASP B:143 , VAL B:144 , THR B:164 , LEU B:165 , ALA B:170 , HOH B:4038BINDING SITE FOR RESIDUE SAH B 4002
3AC3SOFTWARETYR C:12 , TYR C:21 , TYR C:26 , GLY C:64 , SER C:65 , GLY C:66 , THR C:68 , TYR C:70 , ASP C:86 , TYR C:87 , THR C:88 , ASN C:91 , CYS C:142 , ASP C:143 , VAL C:144 , THR C:145 , THR C:164 , LEU C:165 , HOH C:4022 , HOH C:4043BINDING SITE FOR RESIDUE SAH C 4003
4AC4SOFTWARETYR D:12 , TYR D:21 , TYR D:26 , GLY D:64 , SER D:65 , GLY D:66 , THR D:68 , TYR D:70 , ASP D:86 , TYR D:87 , THR D:88 , ASN D:91 , CYS D:142 , ASP D:143 , VAL D:144 , THR D:164 , LEU D:165 , HOH D:4026 , HOH D:4036BINDING SITE FOR RESIDUE SAH D 4004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I62)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn C:121 -Arg C:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I62)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.NNMT_MOUSE8-262
 
 
 
  4A:9-262
B:9-263
C:9-262
D:9-263
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.NNMT_MOUSE59-75
 
 
 
  4A:60-76
B:60-76
C:60-76
D:60-76
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.NNMT_MOUSE8-262
 
 
 
  1A:9-262
-
-
-
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.NNMT_MOUSE59-75
 
 
 
  1A:60-76
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.NNMT_MOUSE8-262
 
 
 
  1-
B:9-263
-
-
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.NNMT_MOUSE59-75
 
 
 
  1-
B:60-76
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.NNMT_MOUSE8-262
 
 
 
  1-
-
C:9-262
-
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.NNMT_MOUSE59-75
 
 
 
  1-
-
C:60-76
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_NNMT_PNMT_TEMTPS51681 SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile.NNMT_MOUSE8-262
 
 
 
  1-
-
-
D:9-263
2NNMT_PNMT_TEMTPS01100 NNMT/PNMT/TEMT family of methyltransferases signature.NNMT_MOUSE59-75
 
 
 
  1-
-
-
D:60-76

(-) Exons   (0, 0)

(no "Exon" information available for 2I62)

(-) 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:257
 aligned with NNMT_MOUSE | O55239 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
           NNMT_MOUSE     5 FTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPG 261
               SCOP domains d2i62a_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2i62A00 A:6-262 Vaccinia Virus protein VP39                                                                                                                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.eeeeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhheeeeee................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeee....eeee..eeee....hhhhhhhhhhhh..eeeeeeee.............eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---SAM_MT_NNMT_PNMT_TEMT  PDB: A:9-262 UniProt: 8-262                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------NNMT_PNMT_TEMT   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i62 A   6 FTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPG 262
                                    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       

Chain B from PDB  Type:PROTEIN  Length:261
 aligned with NNMT_MOUSE | O55239 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:261
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263 
           NNMT_MOUSE     4 GFTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPGRSE 264
               SCOP domains d2i62b_ B: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2i62B00 B:5-265 Vaccinia Virus protein VP39                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.eeeeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhheeeeee................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeee....eeee..eeee....hhhhhhhhhhhh..eeeeeeee.............eeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----SAM_MT_NNMT_PNMT_TEMT  PDB: B:9-263 UniProt: 8-262                                                                                                                                                                                                             -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------NNMT_PNMT_TEMT   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i62 B   5 GFTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPGRSE 265
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 

Chain C from PDB  Type:PROTEIN  Length:258
 aligned with NNMT_MOUSE | O55239 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:258
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253        
           NNMT_MOUSE     4 GFTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPG 261
               SCOP domains d2i62c_ C: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2i62C00 C:5-262 Vaccinia Virus protein VP39                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.eeeeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhheeeeee................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeee....eeee..eeee....hhhhhhhhhhhh..eeeeeeee.............eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----SAM_MT_NNMT_PNMT_TEMT  PDB: C:9-262 UniProt: 8-262                                                                                                                                                                                                             PROSITE (1)
                PROSITE (2) -------------------------------------------------------NNMT_PNMT_TEMT   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i62 C   5 GFTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPG 262
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254        

Chain D from PDB  Type:PROTEIN  Length:259
 aligned with NNMT_MOUSE | O55239 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:259
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         
           NNMT_MOUSE     5 FTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPGRS 263
               SCOP domains d2i62d_ D: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2i62D00 D:6-264 Vaccinia Virus protein VP39                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhh.eeeeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhheeeeee................eeeeeee.hhhhhh.hhhhhhhhhhhhhh.eeeeeeeeeeee....eeee..eeee....hhhhhhhhhhhh..eeeeeeee.............eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---SAM_MT_NNMT_PNMT_TEMT  PDB: D:9-263 UniProt: 8-262                                                                                                                                                                                                             - PROSITE (1)
                PROSITE (2) ------------------------------------------------------NNMT_PNMT_TEMT   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i62 D   6 FTSKDTYLSHFNPRDYLEKYYSFGSRHCAENEILRHLLKNLFKIFCLGAVKGELLIDIGSGPTIYQLLSACESFTEIIVSDYTDQNLWELQKWLKKEPGAFDWSPVVTYVCDLEGNRMKGPEKEEKLRRAIKQVLKCDVTQSQPLGGVSLPPADCLLSTLCLDAACPDLPAYRTALRNLGSLLKPGGFLVMVDALKSSYYMIGEQKFSSLPLGWETVRDAVEEAGYTIEQFEVISQNYSSTTSNNEGLFSLVGRKPGRS 264
                                    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         

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I62)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (NNMT_MOUSE | O55239)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008112    nicotinamide N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine(1+) + nicotinamide = 1-methylnicotinamide + S-adenosyl-L-homocysteine.
    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:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0010243    response to organonitrogen compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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