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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEAR HUMAN NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
 
Authors :  S. Garavaglia, I. D'Angelo, M. Emanuelli, F. Carnevali, F. Pierella, G. Magni, M. Rizzi
Date :  10 Dec 01  (Deposition) - 10 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Alpha/Beta Structure - Rossmann Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Garavaglia, I. D'Angelo, M. Emanuelli, F. Carnevali, F. Pierella, G. Magni, M. Rizzi
Structure Of Human Nmn Adenylyltransferase. A Key Nuclear Enzyme For Nad Homeostasis.
J. Biol. Chem. V. 277 8524 2002
PubMed-ID: 11751893  |  Reference-DOI: 10.1074/JBC.M111589200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
    ChainsA
    EC Number2.7.7.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPT7-7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNMN ADENYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1KKU)

(-) Sites  (0, 0)

(no "Site" information available for 1KKU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (26, 26)

Asymmetric Unit (26, 26)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_068856V9MNMNA1_HUMANDisease (LCA9)387907294AV9M
02UniProtVAR_068857A13TNMNA1_HUMANDisease (LCA9)138613460AA13T
03UniProtVAR_068858I20NNMNA1_HUMANDisease (LCA9)761948762AI20N
04UniProtVAR_068859D33GNMNA1_HUMANDisease (LCA9)  ---AD33G
05UniProtVAR_068860M35TNMNA1_HUMANDisease (LCA9)  ---AM35T
06UniProtVAR_068861A54VNMNA1_HUMANDisease (LCA9)760965874AA54V
07UniProtVAR_068862R66WNMNA1_HUMANDisease (LCA9)763325435AR66W
08UniProtVAR_068863V67FNMNA1_HUMANDisease (LCA9)756903689AV67F
09UniProtVAR_068864M69VNMNA1_HUMANDisease (LCA9)372066126AM69V
10UniProtVAR_068865L72HNMNA1_HUMANDisease (LCA9)  ---AL72H
11UniProtVAR_068866V98GNMNA1_HUMANDisease (LCA9)771336246AV98G
12UniProtVAR_068868V151FNMNA1_HUMANDisease (LCA9)387907292AV151F
13UniProtVAR_068869L153PNMNA1_HUMANDisease (LCA9)  ---AL153P
14UniProtVAR_068870L153VNMNA1_HUMANDisease (LCA9)387907293AL153V
15UniProtVAR_068871G156RNMNA1_HUMANDisease (LCA9)  ---AG156R
16UniProtVAR_068872D173GNMNA1_HUMANDisease (LCA9)  ---AD173G
17UniProtVAR_068873V178MNMNA1_HUMANDisease (LCA9)757724544AV178M
18UniProtVAR_068874Y181CNMNA1_HUMANDisease (LCA9)748913297AY181C
19UniProtVAR_068875I184MNMNA1_HUMANDisease (LCA9)  ---AI184M
20UniProtVAR_068876R207WNMNA1_HUMANDisease (LCA9)142968179AR207W
21UniProtVAR_068877I217NNMNA1_HUMANDisease (LCA9)  ---AF217N
22UniProtVAR_068878R237CNMNA1_HUMANDisease (LCA9)375110174AR237C
23UniProtVAR_068879R237LNMNA1_HUMANDisease (LCA9)368062092AR237L
24UniProtVAR_068880L239SNMNA1_HUMANDisease (LCA9)778606847AL239S
25UniProtVAR_068881H251PNMNA1_HUMANDisease (LCA9)  ---AH251P
26UniProtVAR_068882E257KNMNA1_HUMANDisease (LCA9)150726175AE257K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (26, 156)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_068856V9MNMNA1_HUMANDisease (LCA9)387907294AV9M
02UniProtVAR_068857A13TNMNA1_HUMANDisease (LCA9)138613460AA13T
03UniProtVAR_068858I20NNMNA1_HUMANDisease (LCA9)761948762AI20N
04UniProtVAR_068859D33GNMNA1_HUMANDisease (LCA9)  ---AD33G
05UniProtVAR_068860M35TNMNA1_HUMANDisease (LCA9)  ---AM35T
06UniProtVAR_068861A54VNMNA1_HUMANDisease (LCA9)760965874AA54V
07UniProtVAR_068862R66WNMNA1_HUMANDisease (LCA9)763325435AR66W
08UniProtVAR_068863V67FNMNA1_HUMANDisease (LCA9)756903689AV67F
09UniProtVAR_068864M69VNMNA1_HUMANDisease (LCA9)372066126AM69V
10UniProtVAR_068865L72HNMNA1_HUMANDisease (LCA9)  ---AL72H
11UniProtVAR_068866V98GNMNA1_HUMANDisease (LCA9)771336246AV98G
12UniProtVAR_068868V151FNMNA1_HUMANDisease (LCA9)387907292AV151F
13UniProtVAR_068869L153PNMNA1_HUMANDisease (LCA9)  ---AL153P
14UniProtVAR_068870L153VNMNA1_HUMANDisease (LCA9)387907293AL153V
15UniProtVAR_068871G156RNMNA1_HUMANDisease (LCA9)  ---AG156R
16UniProtVAR_068872D173GNMNA1_HUMANDisease (LCA9)  ---AD173G
17UniProtVAR_068873V178MNMNA1_HUMANDisease (LCA9)757724544AV178M
18UniProtVAR_068874Y181CNMNA1_HUMANDisease (LCA9)748913297AY181C
19UniProtVAR_068875I184MNMNA1_HUMANDisease (LCA9)  ---AI184M
20UniProtVAR_068876R207WNMNA1_HUMANDisease (LCA9)142968179AR207W
21UniProtVAR_068877I217NNMNA1_HUMANDisease (LCA9)  ---AF217N
22UniProtVAR_068878R237CNMNA1_HUMANDisease (LCA9)375110174AR237C
23UniProtVAR_068879R237LNMNA1_HUMANDisease (LCA9)368062092AR237L
24UniProtVAR_068880L239SNMNA1_HUMANDisease (LCA9)778606847AL239S
25UniProtVAR_068881H251PNMNA1_HUMANDisease (LCA9)  ---AH251P
26UniProtVAR_068882E257KNMNA1_HUMANDisease (LCA9)150726175AE257K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003772051aENSE00001473110chr1:10003486-1000357388NMNA1_HUMAN-00--
1.2aENST000003772052aENSE00002202044chr1:10032076-10032246171NMNA1_HUMAN1-39391A:5-3935
1.3ENST000003772053ENSE00001682224chr1:10035650-10035833184NMNA1_HUMAN39-100621A:39-10062
1.4aENST000003772054aENSE00001180526chr1:10041089-10041228140NMNA1_HUMAN100-147481A:100-11011
1.6bENST000003772056bENSE00001473095chr1:10042359-100455563198NMNA1_HUMAN147-2791331A:148-257110

(-) 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:216
 aligned with NMNA1_HUMAN | Q9HAN9 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:253
                                    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   
          NMNA1_HUMAN     5 EKTEVVLLACGSFNPITNMHLRLFELAKDYMNGTGRYTVVKGIISPVGDAYKKKGLIPAYHRVIMAELATKNSKWVEVDTWESLQKEWKETLKVLRHHQEKLEASDCDHQQNSPTLERPGRKRKWTETQDSSQKKSLEPKTKAVPKVKLLCGADLLESFAVPNLWKSEDITQIVANYGLICVTRAGNDAQKFIYESDVLWKHRSNIHVVNEWIANDISSTKIRRALRRGQSIRYLVPDLVQEYIEKHNLYSSE 257
               SCOP domains d1kkua_ A: Nicotinamide mononucleotide (NMN) adenylyltransferase                                                                                                                                                                                              SCOP domains
               CATH domains 1kkuA00 A:5-257 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                         CATH domains
               Pfam domains -------CTP_transf_2-1kkuA01 A:12-229                                                                                                                                                                                             ---------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....hhhhhhhhhhhhhhhhhh..eeeeeeeeee...........hhhhhhhhhhhhhh....eee.hhhhhh....hhhhhhhhhhhhhhh..-------------------------------------..eeeeeehhhhhhhhhh....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhh........hhhhhhhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) ----M---T------N------------G-T------------------V-----------WF-V--H-------------------------G----------------------------------------------------F-P--R----------------G----M--C--M----------------------W---------N-------------------C-S-----------P-----K SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------------------------------------------------------------L-------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:5-39 [INCOMPLETE]------------------------------------------------------------Exon 1.4a  PDB: A:100-110 UniProt: 100-147      -------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.3  PDB: A:39-100 UniProt: 39-100                       ----------------------------------------------Exon 1.6b  PDB: A:148-257 UniProt: 147-279 [INCOMPLETE]                                                         Transcript 1 (2)
                 1kku A   5 EKTEVVLLACGSFNPITNMHLRLFELAKDYMNGTGRYTVVKGIISPVGDAYKKKGLIPAYHRVIMAELATKNSKWVEVDTWESLQKEWKETLKVLRHHQEKLEASD-------------------------------------VPKVKLLCGADLLESFAVPNLWKSEDITQIVANYGLICVTRAGNDAQKFIYESDVLWKHRSNIHVVNEWFANDISSTKIRRALRRGQSIRYLVPDLVQEYIEKHNLYSSE 257
                                    14        24        34        44        54        64        74        84        94       104     |   -         -         -         -   |   154       164       174       184       194       204       214       224       234       244       254   
                                                                                                                                   110                                   148                                                                                                             

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (NMNA1_HUMAN | Q9HAN9)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NMNA1_HUMAN | Q9HAN91gzu 1kqn 1kqo 1kr2

(-) Related Entries Specified in the PDB File

1ej2 1EJ2 CONTAINS THE SAME PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
1f9a 1F9A CONTAINS THE SAME PROTEIN FROM METHANOCOCCUS JANNASCHII