Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  5'-NUCLEOTIDASE FROM E. COLI
 
Authors :  T. Knofel, N. Strater
Date :  16 Sep 98  (Deposition) - 15 Jun 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  5'-Nucleotidase, Udp-Sugar Hydrolase, Phosphatase, Hydrolase (Phosphoric Monoester), Periplasmic Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Knofel, N. Strater
X-Ray Structure Of The Escherichia Coli Periplasmic 5'-Nucleotidase Containing A Dimetal Catalytic Site.
Nat. Struct. Biol. V. 6 448 1999
PubMed-ID: 10331872  |  Reference-DOI: 10.1038/8253

(-) Compounds

Molecule 1 - 5'-NUCLEOTIDASE
    Chains: A
    EC Number: 3.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Taxid: 562
    Gene: USHA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: COMPLEX WITH CARBONATE
    Strain: K12
    Synonym: UDP-SUGAR HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2SO44Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:41 , HIS A:43 , ASP A:84 , GLN A:254 , ZN A:601 , CO3 A:602BINDING SITE FOR RESIDUE ZN A 600
2AC2SOFTWAREASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , ZN A:600 , CO3 A:602BINDING SITE FOR RESIDUE ZN A 601
3AC3SOFTWAREASP A:41 , ASP A:84 , ASN A:116 , HIS A:117 , HIS A:252 , GLN A:254 , THR A:518 , GLY A:519 , ZN A:600 , ZN A:601 , HOH A:1189BINDING SITE FOR RESIDUE CO3 A 602
4AC4SOFTWAREARG A:375 , ARG A:379 , ARG A:410BINDING SITE FOR RESIDUE SO4 A 603
5AC5SOFTWARETRP A:47 , ARG A:48 , HOH A:908 , HOH A:931 , HOH A:1147BINDING SITE FOR RESIDUE SO4 A 604
6AC6SOFTWAREASN A:342 , GLN A:343 , HOH A:628 , HOH A:945BINDING SITE FOR RESIDUE SO4 A 605
7AC7SOFTWARELYS A:68 , GLY A:148 , ARG A:190 , HOH A:862 , HOH A:975 , HOH A:1024 , HOH A:1183BINDING SITE FOR RESIDUE SO4 A 606
8ZNBUNKNOWNASP A:41 , HIS A:43 , ASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , GLN A:254ZN BINDING SITE

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:258 -A:275

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:534 -Pro A:535

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1USH)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
15_NUCLEOTIDASE_1PS00785 5'-nucleotidase signature 1.USHA_ECOLI34-46  1A:34-46
25_NUCLEOTIDASE_2PS00786 5'-nucleotidase signature 2.USHA_ECOLI109-120  1A:109-120

(-) Exons   (0, 0)

(no "Exon" information available for 1USH)

(-) 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:515
 aligned with USHA_ECOLI | P07024 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:525
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545     
           USHA_ECOLI    26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ 550
               SCOP domains d1usha2 A:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1usha1 A:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                              SCOP domains
               CATH domains 1ushA01 A:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1ushA02 A:363-550 5'-nucleotidase;  Domain 2                                                                                                                                                 CATH domains
               Pfam domains --------Metallophos-1ushA01 A:34-256                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------5_nucleotid_C-1ushA02 A:363-511                                                                                                                      --------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee................hhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..hhhhhhhhhh...eee..hhhh...hhhhhhhhhh...eee...eee..........eeeeee..eeeeeeeee...............eee..hhhhhhhhhhhhhhh....eeeeeee....hhh........hhhhhhh.......eee............................eee..eeee.......eeeeeeeeee..eeeeeeeeeee.....----------...........hhhhhhhhhhhhhhhhhhh.eeeee.......hhhh.....hhhhhhhhhhhhhh....eeeehhh.......eeeehhhhhhh.....eeeeeeeehhhhhhhhhhhhh........eeee...eeee..eee.............eeeeeeehhhh..hhh.........eeeeeeehhhhhhhhhhhh....hhhh.....eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ush A  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKK----------RVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ 550
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315     |   -      |335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545     
                                                                                                                                                                                                                                                                                                                                 321        332
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Calcineurin (56)
(-)
Clan: no clan defined [family: 5_nucleotid_C] (8)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (USHA_ECOLI | P07024)
molecular function
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0008768    UDP-sugar diphosphatase activity    Catalysis of the reaction: UDP-sugar + H2O = UMP + sugar 1-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: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:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    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).
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    ZNB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:534 - Pro A:535   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ush
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  USHA_ECOLI | P07024
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.5
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  USHA_ECOLI | P07024
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        USHA_ECOLI | P07024: 1ho5 1hp1 1hpu 1oi8 1oid 1oie 2ush 4wwl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1USH)