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(-) Description

Title :  HUMAN GUANINE DEAMINASE IN COMPLEX WITH VALACYCLOVIR
 
Authors :  M. Welin, L. Egeblad, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Coll A. M. Edwards, S. Flodin, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, T. Kotenyova, M. Moche, T. Nyman, C. Persson, H. Schuler, A. G. Thorsell, L. Tresaugues, J. Weigelt, P. Nordlund
Date :  18 Apr 12  (Deposition) - 02 May 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Purine Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Egeblad, M. Welin, S. Flodin, S. Graslund, L. Wang, J. Balzarini, S. Eriksson, P. Nordlund
Pan-Pathway Based Interaction Profiling Of Fda-Approved Nucleoside And Nucleobase Analogs With Enzymes Of The Human Nucleotide Metabolism.
Plos One V. 7 37724 2012
PubMed-ID: 22662200  |  Reference-DOI: 10.1371/JOURNAL.PONE.0037724

(-) Compounds

Molecule 1 - GUANINE DEAMINASE
    Chains: A
    EC Number: 3.5.4.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PNIC-BSA4
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GUANASE, GUANINE AMINASE, GUANINE AMINOHYDROLASE, GAH, P51-NEDASIN

 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
1TXC1Ligand/Ion2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL L-VALINATE
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TXC2Ligand/Ion2-[(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)METHOXY]ETHYL L-VALINATE
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:82 , HIS A:84 , HIS A:240 , ASP A:330 , TXC A:1452BINDING SITE FOR RESIDUE ZN A1451
2AC2SOFTWAREHIS A:84 , GLN A:87 , LEU A:99 , LEU A:100 , LEU A:103 , ARG A:213 , PHE A:214 , LEU A:216 , HIS A:240 , GLU A:243 , GLU A:247 , ALA A:250 , HIS A:279 , ASP A:330 , ZN A:1451 , HOH A:2033BINDING SITE FOR RESIDUE TXC A1452

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AQL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:331 -Ala A:332
2Val A:448 -Pro A:449

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AQL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AQL)

(-) Exons   (14, 14)

Asymmetric Unit (14, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003583991dENSE00001951441chr9:74764383-74764598216GUAD_HUMAN1-41411A:9-4133
1.3aENST000003583993aENSE00001751942chr9:74810416-7481050489GUAD_HUMAN42-71301A:42-7130
1.5ENST000003583995ENSE00001626863chr9:74817487-74817658172GUAD_HUMAN71-128581A:71-12858
1.6aENST000003583996aENSE00001774554chr9:74825603-7482569088GUAD_HUMAN129-158301A:129-15830
1.7ENST000003583997ENSE00001706302chr9:74828802-74828907106GUAD_HUMAN158-193361A:158-19336
1.9ENST000003583999ENSE00001591719chr9:74834395-7483442228GUAD_HUMAN193-202101A:193-20210
1.10ENST0000035839910ENSE00001722211chr9:74838036-74838143108GUAD_HUMAN203-238361A:203-23836
1.11ENST0000035839911ENSE00001672840chr9:74840593-74840700108GUAD_HUMAN239-274361A:239-27436
1.12aENST0000035839912aENSE00001749359chr9:74842859-7484295698GUAD_HUMAN275-307331A:275-30733
1.13ENST0000035839913ENSE00002175571chr9:74846030-7484609768GUAD_HUMAN307-330241A:307-33024
1.14ENST0000035839914ENSE00001760403chr9:74856068-74856214147GUAD_HUMAN330-379501A:330-37950
1.15ENST0000035839915ENSE00001767251chr9:74860064-74860194131GUAD_HUMAN379-422441A:379-42244
1.16ENST0000035839916ENSE00001624681chr9:74862322-7486234928GUAD_HUMAN423-432101A:423-43210
1.17cENST0000035839917cENSE00001646828chr9:74863188-748671403953GUAD_HUMAN432-454231A:432-45019

(-) 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:442
 aligned with GUAD_HUMAN | Q9Y2T3 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:442
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448  
           GUAD_HUMAN     9 LAHIFRGTFVHSTWTCPMEVLRDHLLGVSDSGKIVFLEEASQQEKLAKEWCFKPCEIRELSHHEFFMPGLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIGNFEVGKEFDAILINPKASDSPIDLFYGDFFGDISEAVIQKFLYLGDDRNIEEVYVGGKQVVPF 450
               SCOP domains d4aqla1 A:9-75,A:389-450 Guanine deaminase                         d4aqla2 A:76-388 Guanine deaminase                                                                                                                                                                                                                                                                                       d4aqla1 A:9-75,A:389-450 Guanine deaminase                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.......eeeeeeeeee.....eeeeee..hhhhhhhhh..hhhhhee.....eeee.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeee.ee............hhhhhhhhhhhhhhhhhhhh...eee..ee......hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh....hhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeehhhhhhhh.....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh................eeee............hhhhhh...hhhhhhhhhhhhhh.eeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1d  PDB: A:9-41           Exon 1.3a  PDB: A:42-71       ---------------------------------------------------------Exon 1.6a  PDB: A:129-158     ----------------------------------Exon 1.9  Exon 1.10  PDB: A:203-238           Exon 1.11  PDB: A:239-274           Exon 1.12a  PDB: A:275-307       ----------------------Exon 1.14  PDB: A:330-379 UniProt: 330-379        -------------------------------------------Exon 1.16 ------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.5  PDB: A:71-128 UniProt: 71-128                   -----------------------------Exon 1.7  PDB: A:158-193            -----------------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:307-33------------------------------------------------Exon 1.15  PDB: A:379-422 UniProt: 379-422  ---------Exon 1.17c          Transcript 1 (2)
                 4aql A   9 LAHIFRGTFVHSTWTCPMEVLRDHLLGVSDSGKIVFLEEASQQEKLAKEWCFKPCEIRELSHHEFFMPGLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIGNFEVGKEFDAILINPKASDSPIDLFYGDFFGDISEAVIQKFLYLGDDRNIEEVYVGGKQVVPF 450
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448
   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  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AQL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AQL)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (GUAD_HUMAN | Q9Y2T3)
molecular function
    GO:0008892    guanine deaminase activity    Catalysis of the reaction: guanine + H2O = xanthine + NH3.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006147    guanine catabolic process    The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.
    GO:0046098    guanine metabolic process    The chemical reactions and pathways involving guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0006195    purine nucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GUAD_HUMAN | Q9Y2T3: 2uz9 3e0l

(-) Related Entries Specified in the PDB File

2uz9 HUMAN GUANINE DEAMINASE (GUAD) IN COMPLEX WITH ZINC AND ITS PRODUCT XHANTINE.