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(-) Description

Title :  HUMAN ADENINE PHOSPHORIBOSYLTRANSFERASE
 
Authors :  O. H. Thiemann, M. Silva, G. Oliva, C. H. T. P. Silva, J. Iulek
Date :  12 Mar 03  (Deposition) - 30 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Human Adenine Phosphoribosyltransferase, Leishmaniasis, Urolithiasis, Glycosyl Transferase, Purine Salvage, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Silva, C. H. T. P. Silva, J. Iulek, O. H. Thiemann
Three-Dimensional Structure Of Human Adenine Phosphoribosyltransferase And Its Relation To Dha-Urolithiasis.
Biochemistry V. 43 7663 2004
PubMed-ID: 15196008  |  Reference-DOI: 10.1021/BI0360758

(-) Compounds

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE
    ChainsA
    EC Number2.4.2.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET29A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GeneAPRT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPRT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:66 , ARG A:67 , ARG A:87 , LYS A:91BINDING SITE FOR RESIDUE CL A 2001
2AC2SOFTWAREVAL A:25 , PHE A:26 , ARG A:27 , ARG A:67 , ASP A:127 , ASP A:128 , LEU A:129 , ALA A:131 , THR A:132 , GLY A:133 , GLY A:134 , THR A:135 , LEU A:159 , HOH A:2002 , HOH A:2024 , HOH A:2028 , HOH A:2070 , HOH A:2109BINDING SITE FOR RESIDUE AMP A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:19 -Pro A:20
2Asp A:65 -Ser A:66
3Ala A:169 -Pro A:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069049L33PAPT_HUMANDisease (APRTD)  ---AL33P
2UniProtVAR_006747D65VAPT_HUMANDisease (APRTD)104894506AD65V
3UniProtVAR_069050V84MAPT_HUMANDisease (APRTD)200392753AV84M
4UniProtVAR_006748L110PAPT_HUMANDisease (APRTD)104894508AL110P
5UniProtVAR_019055Q121RAPT_HUMANPolymorphism8191494AQ121R
6UniProtVAR_069051G133DAPT_HUMANDisease (APRTD)  ---AG133D
7UniProtVAR_006749M136TAPT_HUMANDisease (APRTD)28999113AM136T
8UniProtVAR_022608V150FAPT_HUMANDisease (APRTD)281860266AV150F
9UniProtVAR_022609C153RAPT_HUMANDisease (APRTD)  ---AC153R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (9, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069049L33PAPT_HUMANDisease (APRTD)  ---AL33P
2UniProtVAR_006747D65VAPT_HUMANDisease (APRTD)104894506AD65V
3UniProtVAR_069050V84MAPT_HUMANDisease (APRTD)200392753AV84M
4UniProtVAR_006748L110PAPT_HUMANDisease (APRTD)104894508AL110P
5UniProtVAR_019055Q121RAPT_HUMANPolymorphism8191494AQ121R
6UniProtVAR_069051G133DAPT_HUMANDisease (APRTD)  ---AG133D
7UniProtVAR_006749M136TAPT_HUMANDisease (APRTD)28999113AM136T
8UniProtVAR_022608V150FAPT_HUMANDisease (APRTD)281860266AV150F
9UniProtVAR_022609C153RAPT_HUMANDisease (APRTD)  ---AC153R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT_HUMAN123-135  1A:123-135
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.APT_HUMAN123-135  2A:123-135

(-) Exons   (5, 5)

Asymmetric Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003783641ENSE00001436135chr16:88878342-88878228115APT_HUMAN1-27271A:2-2726
1.2ENST000003783642ENSE00001503918chr16:88878064-88877958107APT_HUMAN27-63371A:27-6337
1.3ENST000003783643ENSE00001503917chr16:88876964-88876831134APT_HUMAN63-107451A:63-10745
1.4ENST000003783644ENSE00001436356chr16:88876556-8887647879APT_HUMAN108-134271A:108-13427
1.5aENST000003783645aENSE00001436502chr16:88876248-88875877372APT_HUMAN134-180471A:134-18047

(-) 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:179
 aligned with APT_HUMAN | P07741 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:179
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         
            APT_HUMAN     2 ADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
               SCOP domains d1orea_ A: Adenine PRTase                                                                                                                                                           SCOP domains
               CATH domains 1oreA00 A:2-180  [code=3.40.50.2020, no name defined]                                                                                                                               CATH domains
               Pfam domains ----------------------------Pribosyltran-1oreA01 A:30-157                                                                                                   ----------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh..eee.........eeehhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhh..eeeeeee.......eeeeeee....eeeeeee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------P-------------------------------V------------------M-------------------------P----------R-----------D--T-------------F--R--------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR--------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:2-27     -----------------------------------Exon 1.3  PDB: A:63-107 UniProt: 63-107      Exon 1.4  PDB: A:108-134   ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.2  PDB: A:27-63 UniProt: 27-63----------------------------------------------------------------------Exon 1.5a  PDB: A:134-180 UniProt: 134-180      Transcript 1 (2)
                 1ore A   2 ADSELQLVEQRIRSFPDFPTPGVVFRDISPVLKDPASFRAAIGLLARHLKATHGGRIDYIAGLDSRGFLFGPSLAQELGLGCVLIRKRGKLPGPTLWASYSLEYGKAELEIQKDALEPGQRVVVVDDLLATGGTMNAACELLGRLQAEVLECVSLVELTSLKGREKLAPVPFFSLLQYE 180
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171         

   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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (APT_HUMAN | P07741)
molecular function
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0002055    adenine binding    Interacting selectively and non-covalently with adenine, a purine base.
    GO:0003999    adenine phosphoribosyltransferase activity    Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
    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.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0046083    adenine metabolic process    The chemical reactions and pathways involving adenine, 6-aminopurine, one of the five main bases found in nucleic acids and a component of numerous important derivatives of its corresponding ribonucleoside, adenosine.
    GO:0006168    adenine salvage    Any process that generates adenine, 6-aminopurine, from derivatives of it without de novo synthesis.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0007625    grooming behavior    The specific behavior of an organism relating to grooming, cleaning and brushing to remove dirt and parasites.
    GO:0007595    lactation    The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

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        APT_HUMAN | P077411opu 1zn7 1zn8 1zn9 4x44 4x45

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