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(-) Description

Title :  5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP
 
Authors :  T. Knoefel, N. Straeter
Date :  12 Dec 00  (Deposition) - 20 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Metallophosphatase, Dinuclear, Metalloenzyme, Hydrolase, Domain Movement (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Knofel, N. Strater
Mechanism Of Hydrolysis Of Phosphate Esters By The Dimetal Center Of 5'-Nucleotidase Based On Crystal Structures.
J. Mol. Biol. V. 309 239 2001
PubMed-ID: 11491293  |  Reference-DOI: 10.1006/JMBI.2001.4656
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-NUCLEOTIDASE
    Chains: A
    EC Number: 3.1.3.5, 3.6.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DS956
    Expression System Taxid: 562
    Gene: USHA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CO31Ligand/IonCARBONATE ION
3SO43Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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: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:949BINDING SITE FOR RESIDUE CO3 A 602
4AC4SOFTWARETRP A:47 , ARG A:48 , HOH A:1196 , HOH A:1223 , HOH A:1224 , HOH A:1381BINDING SITE FOR RESIDUE SO4 A 603
5AC5SOFTWAREASN A:342 , GLN A:343 , HOH A:806 , HOH A:854 , HOH A:1166BINDING SITE FOR RESIDUE SO4 A 604
6AC6SOFTWARELYS A:68 , GLY A:148 , ARG A:190 , HOH A:973 , HOH A:1056 , HOH A:1089 , HOH A:1264 , HOH A:1317BINDING SITE FOR RESIDUE SO4 A 605
7AC7SOFTWAREARG A:375 , ARG A:379 , GLY A:407 , ARG A:410 , PHE A:429 , ASN A:431 , GLY A:458 , PHE A:498 , ASP A:504 , HOH A:1133 , HOH A:1363BINDING SITE FOR RESIDUE ATP A 606

(-) 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 1HP1)

(-) 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 1HP1)

(-) 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:516
 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 d1hp1a2 A:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1hp1a1 A:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                              SCOP domains
               CATH domains 1hp1A01 A:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1hp1A02 A:363-549 5'-nucleotidase;  Domain 2                                                                                                                                               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...............hhhhhhhhhhhhhhhhhhhh.eeeeee.......hhhhhh..hhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhh...ee...eee..........eeeeee..eeeeeeeee...............eee.hhhhhhhhhhhhhhhhh...eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...ee.---------.ee.......hhhhhhhhhhhhhhhhhhh..eeeee......hhhhhh...hhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhh.........eeee.eeeeee..eeeeeee..ee.....eeeeeeehhhhhhhhhh........eeeeeeehhhhhhhhhhhhh..hhhhhh....eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hp1 A  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKK---------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     
                                                                                                                                                                                                                                                                                                                                  322       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  (0, 0)

(no "Pfam Domain" information available for 1HP1)

(-) 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).

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1ho5 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH ADENOSINE AND PHOSPHATE
1hpu 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP
1ush 5'-NUCLEOTIDASE (OPEN FORM), NATIVE
2ush 5'-NUCLEOTIDASE (OPEN FORM), NATIVE