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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'-NUCLEOTIDASE III ( NT5C3)(CASP TARGET)
 
Authors :  K. Wallden, P. Stenmark, C. Arrowsmith, H. Berglund, R. Collins, A. Edw M. Ehn, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, B. M. Hallbe L. Holmberg Schiavone, M. Hogbom, T. Kotenyova, A. Magnusdottir, P. Nilsson-Ehle, T. Nyman, D. Ogg, C. Persson, J. Sagemark, M. Sundstr A. G. Thorsell, J. Uppenberg, S. Van Den Berg, J. Weigelt, M. Welin, P. Nordlund
Date :  17 May 06  (Deposition) - 12 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nucleotide-Binding, Umph1, 5-Prime, Hydrolase, Nucleotidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Wallden, P. Stenmark, T. Nyman, S. Flodin, S. Graslund, P. Loppnau, V. Bianchi, P. Nordlund
Crystal Structure Of Human Cytosolic 5'-Nucleotidase Ii: Insights Into Allosteric Regulation And Substrate Recognition.
J. Biol. Chem. V. 282 17828 2007
PubMed-ID: 17405878  |  Reference-DOI: 10.1074/JBC.M700917200

(-) Compounds

Molecule 1 - CYTOSOLIC 5'-NUCLEOTIDASE III
    ChainsA
    EC Number3.1.3.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP28A-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCN-III, PYRIMIDINE 5'-NUCLEOTIDASE 1, P5'N-1, P5N-1, PN-I, URIDINE 5'-MONOPHOSPHATE HYDROLASE 1, P36

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CN1)

(-) Sites  (0, 0)

(no "Site" information available for 2CN1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CN1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CN1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073160R95G5NT3A_HUMANDisease (P5ND)  ---AR45G
2UniProtVAR_073161C113R5NT3A_HUMANDisease (P5ND)  ---AC63R
3UniProtVAR_023511D137V5NT3A_HUMANDisease (P5ND)104894025AD87V
4UniProtVAR_023512L181P5NT3A_HUMANDisease (P5ND)  ---AL131P
5UniProtVAR_073162G207R5NT3A_HUMANDisease (P5ND)  ---AG157R
6UniProtVAR_023513N229S5NT3A_HUMANDisease (P5ND)104894028AN179S
7UniProtVAR_023514G280R5NT3A_HUMANDisease (P5ND)104894029AG230R
8UniProtVAR_073163I297T5NT3A_HUMANDisease (P5ND)  ---AI247T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_073160R95G5NT3A_HUMANDisease (P5ND)  ---AR45G
2UniProtVAR_073161C113R5NT3A_HUMANDisease (P5ND)  ---AC63R
3UniProtVAR_023511D137V5NT3A_HUMANDisease (P5ND)104894025AD87V
4UniProtVAR_023512L181P5NT3A_HUMANDisease (P5ND)  ---AL131P
5UniProtVAR_073162G207R5NT3A_HUMANDisease (P5ND)  ---AG157R
6UniProtVAR_023513N229S5NT3A_HUMANDisease (P5ND)104894028AN179S
7UniProtVAR_023514G280R5NT3A_HUMANDisease (P5ND)104894029AG230R
8UniProtVAR_073163I297T5NT3A_HUMANDisease (P5ND)  ---AI247T

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CN1)

(-) Exons   (8, 8)

Asymmetric Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002422101aENSE00002172001chr7:33102409-331021802305NT3A_HUMAN1-51510--
1.5bENST000002422105bENSE00001756142chr7:33066527-33066429995NT3A_HUMAN52-84331A:14-3421
1.6bENST000002422106bENSE00001650087chr7:33063720-33063651705NT3A_HUMAN85-108241A:35-5824
1.7aENST000002422107aENSE00001744550chr7:33061711-33061665475NT3A_HUMAN108-123161A:58-7316
1.8ENST000002422108ENSE00001625828chr7:33060969-33060884865NT3A_HUMAN124-152291A:74-10229
1.9ENST000002422109ENSE00001781106chr7:33059336-33059247905NT3A_HUMAN152-182311A:102-13231
1.10aENST0000024221010aENSE00001601096chr7:33057213-330570511635NT3A_HUMAN182-236551A:132-18655
1.11bENST0000024221011bENSE00001627659chr7:33055482-330552822015NT3A_HUMAN237-303671A:187-25367
1.12dENST0000024221012dENSE00001938905chr7:33054443-330537606845NT3A_HUMAN304-336331A:254-28633

(-) 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:273
 aligned with 5NT3A_HUMAN | Q9H0P0 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:273
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333   
          5NT3A_HUMAN    64 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL 336
               SCOP domains d2cn1a1 A:14-286 Cytosolic 5'-nucleotidase III                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeee.........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.......hhhhhhhhhhh....eeeeeeeehhhhhhhhhhh......eeeeee.eee.....eeee........hhhhhhhhhhhhhhh.....eeeeee..hhhhhh........eeeeeeee..hhhhhhhhhhh...eeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------G-----------------R-----------------------V-------------------------------------------P-------------------------R---------------------S--------------------------------------------------R----------------T--------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5b            Exon 1.6b  PDB: A:35-58 ---------------Exon 1.8  PDB: A:74-102      -----------------------------Exon 1.10a  PDB: A:132-186 UniProt: 182-236            Exon 1.11b  PDB: A:187-253 UniProt: 237-303                        Exon 1.12d  PDB: A:254-286        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.7a       ----------------------------Exon 1.9  PDB: A:102-132       ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2cn1 A  14 NPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDECRKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVMLKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLKGFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL 286
                                    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       273       283   

   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  (0, 0)

(no "CATH Domain" information available for 2CN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CN1)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (5NT3A_HUMAN | Q9H0P0)
molecular function
    GO:0008665    2'-phosphotransferase activity    Catalysis of the transfer of a phosphate group from one compound to the 2' position of another.
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0046085    adenosine metabolic process    The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0046135    pyrimidine nucleoside catabolic process    The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0006213    pyrimidine nucleoside metabolic process    The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
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.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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)

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        5NT3A_HUMAN | Q9H0P02jga 2vkq

(-) Related Entries Specified in the PDB File

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