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(-) Description

Title :  5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE AND PHOSPHATE
 
Authors :  T. Knoefel, N. Straeter
Date :  08 Dec 00  (Deposition) - 20 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metalloprotein, Domain Movement, Hydrolase (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
    ChainsA, B
    EC Number3.1.3.5, 3.6.1.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainDS956
    Expression System Taxid562
    GeneUSHA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2MN4Ligand/IonMANGANESE (II) ION
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2MN-1Ligand/IonMANGANESE (II) ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADN1Ligand/IonADENOSINE
2MN-1Ligand/IonMANGANESE (II) ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:41 , HIS A:43 , ASP A:84 , GLN A:254 , MN A:1602 , HOH A:1775 , HOH A:1823BINDING SITE FOR RESIDUE MN A 1601
2AC2SOFTWAREASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , MN A:1601 , PO4 A:1603 , HOH A:1823BINDING SITE FOR RESIDUE MN A 1602
3AC3SOFTWAREASP A:84 , ASN A:116 , HIS A:117 , HIS A:252 , ARG A:375 , MN A:1602 , ADN A:1604 , HOH A:1741 , HOH A:1775 , HOH A:1823BINDING SITE FOR RESIDUE PO4 A 1603
4AC4SOFTWAREASP B:41 , HIS B:43 , ASP B:84 , GLN B:254 , MN B:2602 , HOH B:2704BINDING SITE FOR RESIDUE MN B 2601
5AC5SOFTWAREASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , MN B:2601 , PO4 B:2603 , HOH B:2704BINDING SITE FOR RESIDUE MN B 2602
6AC6SOFTWAREASP B:84 , ASN B:116 , HIS B:117 , ILE B:178 , HIS B:252 , MN B:2602 , ADN B:2604 , HOH B:2704 , HOH B:2718BINDING SITE FOR RESIDUE PO4 B 2603
7AC7SOFTWAREILE A:178 , SER A:405 , GLY A:407 , PHE A:429 , ASN A:431 , GLY A:458 , PHE A:498 , ASP A:504 , PO4 A:1603 , HOH A:1756BINDING SITE FOR RESIDUE ADN A 1604
8AC8SOFTWAREILE B:178 , ASN B:180 , SER B:405 , GLY B:407 , ARG B:410 , PHE B:429 , ASN B:431 , GLY B:458 , PHE B:498 , ASP B:504 , PO4 B:2603 , HOH B:2718BINDING SITE FOR RESIDUE ADN B 2604

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:258 -A:275
2B:258 -B:275

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:534 -Pro A:535
2Ser B:534 -Pro B:535

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HO5)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
15_NUCLEOTIDASE_1PS00785 5'-nucleotidase signature 1.USHA_ECOLI34-46
 
  2A:34-46
B:34-46
25_NUCLEOTIDASE_2PS00786 5'-nucleotidase signature 2.USHA_ECOLI109-120
 
  2A:109-120
B:109-120
Biological Unit 1 (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
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
15_NUCLEOTIDASE_1PS00785 5'-nucleotidase signature 1.USHA_ECOLI34-46
 
  1-
B:34-46
25_NUCLEOTIDASE_2PS00786 5'-nucleotidase signature 2.USHA_ECOLI109-120
 
  1-
B:109-120

(-) Exons   (0, 0)

(no "Exon" information available for 1HO5)

(-) 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:525
 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 d1ho5a2 A:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1ho5a1 A:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                              SCOP domains
               CATH domains 1ho5A01 A:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1ho5A02 A:363-549 5'-nucleotidase;  Domain 2                                                                                                                                               - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee...............hhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhh..hhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhh...ee...eee..........eeeeee..eeeeeeeee..hhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhhh...eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhhh.eeeee......hhhhhh...hhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhhh........eeee..............ee..ee.....eeeeeeehhhhhhhhhh.........eeeeeehhhhhhhhhhhhh..hhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ho5 A  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ 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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545     

Chain B from PDB  Type:PROTEIN  Length:525
 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 d1ho5b2 B:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1ho5b1 B:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                              SCOP domains
               CATH domains 1ho5B01 B:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1ho5B02 B: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....ee....eeeeee..eeeeeeeee..hhhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh...eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhhh.eeeee......hhhhhh...hhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhh.........eeee....eee..eee..ee..ee.....eeeeeeehhhhhhhhhh........eeeeeeehhhhhhhhhhhhh..hhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ho5 B  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ 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       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545     

   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, 4)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HO5)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 | P070241hp1 1hpu 1oi8 1oid 1oie 1ush 2ush 4wwl

(-) Related Entries Specified in the PDB File

1hp1 5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP
1hpu 5'-NT CLOSED CONFORMATION, COMPLEX WITH AMPCP
1ush 5'-NT OPEN CONFORMATION, TETRAGONAL CRYSTAL FORM
2ush 5'-NT OPEN CONFORMATION, ORTHORHOMBIC CRYSTAL FORM