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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NAMN ADENYLYLTRANSFERASE COMPLEXED WITH NAAD
 
Authors :  X. Zhang, O. V. Kurnasov, S. Karthikeyan, N. V. Grishin, A. L. Osterman,
Date :  01 Feb 03  (Deposition) - 03 Jun 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Nad Biosynthesis, Mitochondria, Pyridine Adenylyltransferase, Enzyme Catalysis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhang, O. V. Kurnasov, S. Karthikeyan, N. V. Grishin, A. L. Osterman H. Zhang
Structural Characterization Of A Human Cytosolic Nmn/Namn Adenylyltransferase And Implication In Human Nad Biosynthesis
J. Biol. Chem. V. 278 13503 2003
PubMed-ID: 12574164  |  Reference-DOI: 10.1074/JBC.M300073200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FKSG76
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX
    Expression System Strain: DH10-BETA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FKSG76
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NMN/NAMN ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1NXX2Ligand/Ion1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-3-CARBOXYPYRIDINIUM
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1NXX4Ligand/Ion1-[(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]-3-CARBOXYPYRIDINIUM
2SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , ARG A:98 , HIS A:152 , HOH A:694BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARELYS A:56 , ALA A:202 , THR A:203 , HOH A:645 , LYS B:140BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWARECYS A:12 , GLY A:13 , SER A:14 , PHE A:15 , MET A:21 , HIS A:22 , TYR A:53 , TRP A:90 , GLU A:92 , THR A:93 , CYS A:134 , GLY A:135 , ASP A:137 , VAL A:138 , LEU A:147 , TRP A:148 , ARG A:167 , ASN A:198 , HOH A:512 , HOH A:519 , HOH A:534 , HOH A:549 , HOH A:573 , HOH A:589 , HOH A:692 , HOH A:745BINDING SITE FOR RESIDUE NXX A 401
4AC4SOFTWARELYS B:95 , ARG B:98 , HIS B:152 , HOH B:774BINDING SITE FOR RESIDUE SO4 B 303
5AC5SOFTWARELYS A:140 , SER B:201 , ALA B:202 , THR B:203 , HOH B:726BINDING SITE FOR RESIDUE SO4 B 304
6AC6SOFTWARECYS B:12 , GLY B:13 , SER B:14 , PHE B:15 , MET B:21 , HIS B:22 , VAL B:49 , TYR B:53 , TRP B:90 , GLU B:92 , THR B:93 , CYS B:134 , GLY B:135 , ASP B:137 , VAL B:138 , LEU B:147 , TRP B:148 , ARG B:167 , ASN B:198 , GLU B:199 , HOH B:504 , HOH B:543 , HOH B:563 , HOH B:572 , HOH B:583 , HOH B:614 , HOH B:674 , HOH B:726BINDING SITE FOR RESIDUE NXX B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:16 -Pro A:17
2Asn B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1gENST000002962021gENSE00002030268chr3:139396788-139396547242NMNA3_HUMAN-00--
1.3ENST000002962023ENSE00001259240chr3:139356904-139356805100NMNA3_HUMAN-00--
1.5aENST000002962025aENSE00002150136chr3:139346606-139346458149NMNA3_HUMAN1-37372A:3-37
B:3-37		35
35
1.8ENST000002962028ENSE00001593512chr3:139297897-139297714184NMNA3_HUMAN37-98622A:37-98
B:37-98		62
62
1.10bENST0000029620210bENSE00001788543chr3:139292522-13929244083NMNA3_HUMAN98-126292A:98-126 (gaps)
B:98-106		29
9
1.12eENST0000029620212eENSE00002054810chr3:139280234-139279424811NMNA3_HUMAN126-2521272A:126-235
B:127-234		110
108

(-) 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:213
 aligned with NMNA3_HUMAN | Q96T66 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:233
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   
          NMNA3_HUMAN     3 SRIPVVLLACGSFNPITNMHLRMFEVARDHLHQTGMYQVIQGIISPVNDTYGKKDLAASHHRVAMARLALQTSDWIRVDPWESEQAQWMETVKVLRHHHSKLLRSPPQMEGPDHGKALFSTPAAVPELKLLCGADVLKTFQTPNLWKDAHIQEIVEKFGLVCVGRVGHDPKGYIAESPILRMHQHNIHLAKEPVQNEISATYIRRALGQGQSVKYLIPDAVITYIKDHGLYTK 235
               SCOP domains d1nuqa_ A: Cytosolic NMN/NAMN adenylyltransferase                                                                                                                                                                                         SCOP domains
               CATH domains 1nuqA00 A:3-235 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhhh--------------------...eeeeeeehhhhhhh......hhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhh........hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: A:3-37 [INCOMPLETE]------------------------------------------------------------Exon 1.10b UniProt: 98-126   ------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.8  PDB: A:37-98 UniProt: 37-98                         ---------------------------Exon 1.12e  PDB: A:126-235 UniProt: 126-252 [INCOMPLETE]                                                       Transcript 1 (2)
                 1nuq A   3 SRIPVVLLACGSFNPITNMHLRMFEVARDHLHQTGMYQVIQGIISPVNDTYGKKDLAASHHRVAMARLALQTSDWIRVDPWESEQAQWMETVKVLRHHHSKLL--------------------AVPELKLLCGADVLKTFQTPNLWKDAHIQEIVEKFGLVCVGRVSHDPKGYIAESPILRMHQHNIHLAKEPVQNEISATYIRRALGQGQSVKYLIPDAVITYIKDHGLYTK 235
                                    12        22        32        42        52        62        72        82        92       102  |      -         -   |   132       142       152       162       172       182       192       202       212       222       232   
                                                                                                                                105                  126                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with NMNA3_HUMAN | Q96T66 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:232
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
          NMNA3_HUMAN     3 SRIPVVLLACGSFNPITNMHLRMFEVARDHLHQTGMYQVIQGIISPVNDTYGKKDLAASHHRVAMARLALQTSDWIRVDPWESEQAQWMETVKVLRHHHSKLLRSPPQMEGPDHGKALFSTPAAVPELKLLCGADVLKTFQTPNLWKDAHIQEIVEKFGLVCVGRVGHDPKGYIAESPILRMHQHNIHLAKEPVQNEISATYIRRALGQGQSVKYLIPDAVITYIKDHGLYT 234
               SCOP domains d1nuqb_ B: Cytosolic NMN/NAMN adenylyltransferase                                                                                                                                                                                        SCOP domains
               CATH domains 1nuqB00 B:3-234 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                    CATH domains
           Pfam domains (1) -------CTP_transf_2-1nuqB01 B:10-208                                                                                                                                                                          -------------------------- Pfam domains (1)
           Pfam domains (2) -------CTP_transf_2-1nuqB02 B:10-208                                                                                                                                                                          -------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeeeeeeee...........hhhhhhhhhhhhhh....eee..hhhhh....hhhhhhhhhhhhhhh--------------------..eeeeeeehhhhhhh......hhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhh........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5a  PDB: B:3-37 [INCOMPLETE]------------------------------------------------------------Exon 1.10b  PDB: B:98-106    ------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.8  PDB: B:37-98 UniProt: 37-98                         ---------------------------Exon 1.12e  PDB: B:127-234 UniProt: 126-252 [INCOMPLETE]                                                      Transcript 1 (2)
                 1nuq B   3 SRIPVVLLACGSFNPITNMHLRMFEVARDHLHQTGMYQVIQGIISPVNDTYGKKDLAASHHRVAMARLALQTSDWIRVDPWESEQAQWMETVKVLRHHHSKLLR--------------------VPELKLLCGADVLKTFQTPNLWKDAHIQEIVEKFGLVCVGRVSHDPKGYIAESPILRMHQHNIHLAKEPVQNEISATYIRRALGQGQSVKYLIPDAVITYIKDHGLYT 234
                                    12        22        32        42        52        62        72        82        92       102   |     -         -    |  132       142       152       162       172       182       192       202       212       222       232  
                                                                                                                                 106                  127
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NMNA3_HUMAN | Q96T66)
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:0004515    nicotinate-nucleotide adenylyltransferase activity    Catalysis of the reaction: ATP + nicotinate ribonucleotide = diphosphate + deamido-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:0034628    'de novo' NAD biosynthetic process from aspartate    The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
    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:0019674    NAD metabolic process    The chemical reactions and pathways involving nicotinamide adenine dinucleotide (NAD), a coenzyme present in most living cells and derived from the B vitamin nicotinic acid.
    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.
    GO:0009611    response to wounding    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 stimulus indicating damage to the organism.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NMNA3_HUMAN | Q96T66: 1nup 1nur 1nus 1nut 1nuu

(-) Related Entries Specified in the PDB File

1nup THE SAME PROTEIN COMPLEXED WITH NMN
1nur THE SAME PROTEIN
1nus THE SAME PROTEIN COMPLEXED WITH NMN AND ATP ANALOG
1nut THE SAME PROTEIN COMPLEXED WITH ATP ANALOG
1nuu THE SAME PROTEIN COMPLEXED WITH NAD