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(-) Description

Title :  RE-INVESTIGATED HIGH RESOLUTION CRYSTAL STRUCTURE OF HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN 1 (HINT1) FROM RABBIT COMPLEXED WITH ADENOSINE
 
Authors :  R. M. Dolot, M. Ozga, A. Krakowiak, B. Nawrot, W. J. Stec
Date :  25 Jan 11  (Deposition) - 16 Feb 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hint Protein, Hit Family Protein, Hydrolase, Adenosine 5'- Monophosphoramidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Dolot, M. Ozga, A. Krakowiak, B. Nawrot
High-Resolution X-Ray Crystal Structure Of Rabbit Histidine Triad Nucleotide-Binding Protein 1 (Rhint1) - Adenosine Complex At 1. 10A Resolution
Acta Crystallogr. , Sect. D V. 67 601 2011
PubMed-ID: 21697598  |  Reference-DOI: 10.1107/S0907444911015605

(-) Compounds

Molecule 1 - HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN 1
    ChainsA
    EC Number3.-.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSGO2
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneHINT1, HINT
    Organism CommonEUROPEAN RABBIT,JAPANESE WHITE RABBIT,DOMESTIC RABBIT,RABBITS
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymADENOSINE 5'-MONOPHOSPHORAMIDASE, P13.7

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:18 , PHE A:19 , LYS A:25 , GLU A:34 , HIS A:42 , ASP A:43 , ILE A:44 , SER A:45 , LEU A:53 , HIS A:112 , HIS A:114 , HOH A:148 , HOH A:162 , HOH A:175 , HOH A:179 , HOH A:188 , HOH A:201 , HOH A:240BINDING SITE FOR RESIDUE ADN A 127

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QGZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QGZ)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIT_2PS51084 HIT domain profile.HINT1_RABIT18-126  1A:18-126
2HIT_1PS00892 HIT domain signature.HINT1_RABIT99-117  1A:99-117
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HIT_2PS51084 HIT domain profile.HINT1_RABIT18-126  2A:18-126
2HIT_1PS00892 HIT domain signature.HINT1_RABIT99-117  2A:99-117

(-) Exons   (0, 0)

(no "Exon" information available for 3QGZ)

(-) 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:114
 aligned with HINT1_RABIT | P80912 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:114
                                    22        32        42        52        62        72        82        92       102       112       122    
          HINT1_RABIT    13 PGGDTIFGKIIRKEIPAKIIFEDDQCLAFHDISPQAPTHFLVIPKKHISQISAAEDADESLLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG 126
               SCOP domains d3qgza_ A: Histidine triad nucleotide-binding protein (HINT)                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------HIT-3qgzA01 A:24-121                                                                              ----- Pfam domains
         Sec.struct. author ....hhhhhhhh......eeee...eeeee.......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..hhhhhh.......eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----HIT_2  PDB: A:18-126 UniProt: 18-126                                                                          PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------HIT_1  PDB: A:99-11--------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3qgz A  13 PGGDTIFGKIIRKEIPAKIIFEDDQCLAFHDISPQAPTHFLVIPKKHISQISAAEDADESLLGHLMIVGKKCAADLGLKKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMNWPPG 126
                                    22        32        42        52        62        72        82        92       102       112       122    

   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 3QGZ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HIT (23)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (HINT1_RABIT | P80912)
molecular function
    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: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: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.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0072332    intrinsic apoptotic signaling pathway by p53 class mediator    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, and ends when the execution phase of apoptosis is triggered.
    GO:0009154    purine ribonucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    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
        HINT1_RABIT | P809121rzy 3o1c 3o1x 3o1z 3rhn 4rhn 5rhn 6rhn

(-) Related Entries Specified in the PDB File

1rzy THE SAME PROTEIN COMPLEXED WITH 8-ETHYLSULPHAMOYLADENOSINE
3llj CRYSTAL STRUCTURE OF HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN 1 (HINT1) FROM RABBIT COMPLEXED WITH ADENOSINE
3rhn THE SAME PROTEIN COMPLEXED WITH GMP
4rhn THE SAME PROTEIN COMPLEXED WITH AMP
5rhn THE SAME PROTEIN COMPLEXED WITH 8-BR-AMP
6rhn THE SAME PROTEIN IN NATIVE STATE