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(-) Description

Title :  CRYSTAL STRUCTURE OF 5'-NUCLEOTIDASE PRECURSOR FROM THERMUS THERMOPHILUS HB8
 
Authors :  N. Nakagawa, S. Kishishita, S. Yokoyama, S. Kuramitsu, Riken Structu Genomics/Proteomics Initiative (Rsgi)
Date :  08 May 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Nucleotidase, Metal-Binding, Nucleotide-Binding, Hydrolase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Nakakaga, S. Kishishita, S. Yokoyama, S. Kuramitsu
Crystal Structure Of 5'-Nucleotidase Precursor From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5'-NUCLEOTIDASE
    Chains: A
    EC Number: 3.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2THM1Ligand/IonTHYMIDINE
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:39 , ASP A:83 , ASN A:115 , HIS A:116 , HIS A:238 , HIS A:240 , ARG A:345 , ARG A:349 , ARG A:383 , ZN A:5647 , ZN A:5648 , THM A:6510 , HOH A:6559 , HOH A:7097BINDING SITE FOR RESIDUE PO4 A 5646
2AC2SOFTWAREASP A:37 , HIS A:39 , ASP A:83 , HIS A:240 , PO4 A:5646 , ZN A:5648 , HOH A:6559BINDING SITE FOR RESIDUE ZN A 5647
3AC3SOFTWAREASP A:83 , ASN A:115 , HIS A:215 , HIS A:238 , PO4 A:5646 , ZN A:5647 , HOH A:6559BINDING SITE FOR RESIDUE ZN A 5648
4AC4SOFTWAREASN A:115 , HIS A:116 , ASP A:119 , ILE A:179 , ASN A:181 , ASN A:378 , GLY A:380 , GLY A:381 , PHE A:402 , ASN A:404 , GLY A:432 , PHE A:481 , ASP A:487 , PO4 A:5646 , HOH A:6623 , HOH A:6658BINDING SITE FOR RESIDUE THM A 6510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z1A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:257 -Pro A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z1A)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z1A)

(-) Sequences/Alignments

Asymmetric/Biological 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:507
 aligned with Q5SIP1_THET8 | Q5SIP1 from UniProtKB/TrEMBL  Length:552

    Alignment length:507
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       
         Q5SIP1_THET8    28 FTLTLVHTNDTHAHLEPVELTLSGEKTPVGGVARRVALFDRVWARAKNPLFLDAGDVFQGTLYFNQYRGLADRYFMHRLRYRAMALGNHEFDLGPGPLADFLKGARFKVVSANVDASREPRLKGLFAPYAVVVVGGERVGIIGLTTPDTREISNPGPTVAFLDPYESAQKAVYELLAKGVNKIVVLSHLGYGEDLKLARRLVGVQVIVGGHSHTLLGSFPHKELSPAGPYPTVVKNPEGKDVLVVQAWEWGKVVGLLEVTFDAKGELLAYKGEALLMTPEAAPEDFFAKEALLAYAQPVMALMQQVIAEAKVDLVGERAVVRRRESNLGNLITDGMLWKTRNAGTQIALQNGGGIRASIPKGPITVGKVYEVLPFGNTLVVMDLKGKEILAALENGVSQWENTAGRFLQVSGLRYAFDLSRPAGSRVVRVEVKTEKGYVPLDLEATYRVVVNNFIANGGDGFTVLKEAQGYRVDTGFSDAESFMDYLKELKVVEAGLEGRIEVLNEP 534
               SCOP domains d2z1aa2 A:28-329 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                d2z1aa1 A:330-534 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.........eeee....eeee.hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh...eee.hhhhhh.hhhhhhhhhh....eee...ee...hhhhh.....eeeeee..eeeeeeeee..hhhhhh......ee.hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhh......eeee......................eeee.....eeeeee......eeeeeeeee.....eeeeeeeeee........hhhhhhhhhhhhh.hhhhhhheeeee......hhhhhh...hhhhhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhhhhhhhh....eeee.eeeeee........eeeeeeee..eeee.....eeeeeeehhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhee.......eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z1a A  28 FTLTLVHTNDTHAHLEPVELTLSGEKTPVGGVARRVALFDRVWARAKNPLFLDAGDVFQGTLYFNQYRGLADRYFMHRLRYRAMALGNHEFDLGPGPLADFLKGARFKVVSANVDASREPRLKGLFAPYAVVVVGGERVGIIGLTTPDTREISNPGPTVAFLDPYESAQKAVYELLAKGVNKIVVLSHLGYGEDLKLARRLVGVQVIVGGHSHTLLGSFPHKELSPAGPYPTVVKNPEGKDVLVVQAWEWGKVVGLLEVTFDAKGELLAYKGEALLMTPEAAPEDFFAKEALLAYAQPVMALMQQVIAEAKVDLVGERAVVRRRESNLGNLITDGMLWKTRNAGTQIALQNGGGIRASIPKGPITVGKVYEVLPFGNTLVVMDLKGKEILAALENGVSQWENTAGRFLQVSGLRYAFDLSRPAGSRVVRVEVKTEKGYVPLDLEATYRVVVNNFIANGGDGFTVLKEAQGYRVDTGFSDAESFMDYLKELKVVEAGLEGRIEVLNEP 534
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z1A)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5SIP1_THET8 | Q5SIP1)
molecular function
    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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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.
biological process
    GO:0009166    nucleotide catabolic process    The chemical reactions and pathways resulting in the breakdown of nucleotides, any 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).

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