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(-) Description

Title :  5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (S228C, P513C)
 
Authors :  R. Schultz-Heienbrok, T. Maier, N. Straeter
Date :  13 Jun 03  (Deposition) - 10 Jun 04  (Release) - 13 Jul 11  (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, Hydrolase, Domain Movement, Disulfide Engineering, Udp-Sugar Hydrolase, Conformational Trapping (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Schultz-Heienbrok, T. Maier, N. Straeter
Trapping A 96 Degree Domain Rotation In Two Distinct Conformations By Engineered Disulfide Bridges
Protein Sci. V. 13 1811 2004
PubMed-ID: 15215524  |  Reference-DOI: 10.1110/PS.04629604
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN USHA
    ChainsA, B
    EC Number3.1.3.5, 3.6.1.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainER2566
    Expression System Taxid562
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsDISULFIDE CROSSLINK BETWEEN N- AND C-TERMINAL DOMAINS
    Synonym5-NUCLEOTIDASE

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , HOH A:2114 , HOH A:2238BINDING SITE FOR RESIDUE NI A1551

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:228 -A:513
2A:258 -A:275
3B:228 -B:513
4B: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 1OID)

(-) 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 1OID)

(-) 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 d1oida2 A:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1oida1 A:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                              SCOP domains
               CATH domains 1oidA01 A:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1oidA02 A:363-550 5'-nucleotidase;  Domain 2                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...............hhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhh..hhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhh...ee...eee..........eeeeee..eeeeeeeee..hhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhh....eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh..eeeee......hhhhhh...hhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhh.........eeee.eeeee....eeeeee..ee.....eeeeeeehhhhhhhhhh........eeeeeeehhhhhhhhhhhhh..hhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oid A  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGCNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKCGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ 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:523
 aligned with USHA_ECOLI | P07024 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:523
                                    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 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVS 548
               SCOP domains d1oidb2 B:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1oidb1 B:363-548 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                            SCOP domains
               CATH domains 1oidB01 B:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1oidB02 B:363-548 5'-nucleotidase;  Domain 2                                                                                                                                               CATH domains
           Pfam domains (1) --------Metallophos-1oidB01 B:34-256                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------5_nucleotid_C-1oidB03 B:363-511                                                                                                                      ------------------------------------- Pfam domains (1)
           Pfam domains (2) --------Metallophos-1oidB02 B:34-256                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------5_nucleotid_C-1oidB04 B:363-511                                                                                                                      ------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeeeeee...............hhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhh..hhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhh...ee...eee..........eeeeee..eeeeeeeee.hhhhhh........eee.hhhhhhhhhhhhhhhh....eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhh...hhhhhhhhhhhhhhhh..eeeee..........eeeehhhhhhhh....eeeeeeehhhhhhhhhhhhh.........eeee.ee...........ee..ee......eeeeeehhhhhhhhhh........eeeeeeehhhhhhhhhhhh..ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oid B  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGCNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKCGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVS 548
                                    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  (2, 4)

Asymmetric Unit

(-) 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 | P070241ho5 1hp1 1hpu 1oi8 1oie 1ush 2ush 4wwl

(-) Related Entries Specified in the PDB File

1ho5 5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE ANDPHOSPHATE
1hp1 5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP
1hpu 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP
1oi8 5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (P90C, L424C)
1oie 5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (S228C, P513C)
1ush 5'-NUCLEOTIDASE FROM E. COLI
2ush 5'-NUCLEOTIDASE FROM E. COLI