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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE HYDROLASE FROM LEISHMANIA MAJOR
 
Authors :  W. Shi, V. L. Schramm, S. C. Almo
Date :  11 May 00  (Deposition) - 24 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Shi, V. L. Schramm, S. C. Almo
Nucleoside Hydrolase From Leishmania Major. Cloning, Expression, Catalytic Properties, Transition State Inhibitors, And The 2. 5-A Crystal Structure.
J. Biol. Chem. V. 274 21114 1999
PubMed-ID: 10409664  |  Reference-DOI: 10.1074/JBC.274.30.21114
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOSIDE HYDROLASE
    Chains: A, B, C, D
    EC Number: 3.2.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMW172
    Expression System Taxid: 562
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , ASP A:15 , THR A:126 , ASP A:241BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREASP B:10 , ASP B:15 , THR B:126 , ASP B:241BINDING SITE FOR RESIDUE CA B 401
3AC3SOFTWAREASP C:10 , ASP C:15 , THR C:126 , ASP C:241BINDING SITE FOR RESIDUE CA C 401
4AC4SOFTWAREASP D:10 , ASP D:15 , THR D:126 , ASP D:241BINDING SITE FOR RESIDUE CA D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EZR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EZR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IUNHPS01247 Inosine-uridine preferring nucleoside hydrolase family signature.IUNH_LEIMA8-18
 
 
 		  4A:8-18
B:8-18
C:8-18
D:8-18

(-) Exons   (0, 0)

(no "Exon" information available for 1EZR)

(-) 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:312
 aligned with IUNH_LEIMA | P83851 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
           IUNH_LEIMA     2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHQALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVVDFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
               SCOP domains d1ezra_ A: Nucleoside hydrolase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ezrA00 A:2-313 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh......eee......................................hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh.hhhhhh.eeeee.............hhhhhhhhhhhhhhhh....eeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeee...eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------IUNH       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ezr A   2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHLALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVADFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  


Chain B from PDB  Type:PROTEIN  Length:312
 aligned with IUNH_LEIMA | P83851 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
           IUNH_LEIMA     2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHQALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVVDFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
               SCOP domains d1ezrb_ B: Nucleoside hydrolase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ezrB00 B:2-313 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh......eee......................................hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh.hhhhhh.eeeee.............hhhhhhhhhhhhhhhh....eeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeee...eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------IUNH       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ezr B   2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHLALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVADFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  


Chain C from PDB  Type:PROTEIN  Length:312
 aligned with IUNH_LEIMA | P83851 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
           IUNH_LEIMA     2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHQALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVVDFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
               SCOP domains d1ezrc_ C: Nucleoside hydrolase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ezrC00 C:2-313 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh......eee......................................hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhhhhhhhhh....eeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeee...eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------IUNH       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ezr C   2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHLALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVADFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  


Chain D from PDB  Type:PROTEIN  Length:312
 aligned with IUNH_LEIMA | P83851 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
           IUNH_LEIMA     2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHQALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVVDFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
               SCOP domains d1ezrd_ D: Nucleoside hydrolase                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1ezrD00 D:2-313 Inosine-uridine Nucleoside N-ribohydrolase, chain A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhh......eee......................................hhhhhhhhhhhhh....eeeee...hhhhhhhhhhh.hhhhhh.eeeee.............hhhhhhhhhhhhhhhh....eeeehhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...eeeee..eee..........eee...........eeeeeeehhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------IUNH       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ezr D   2 PRKIILDCDPGIDDAVAIFLAHGNPEIELLAITTVVGNQSLEKVTQNARLVADVAGIVGVPVAAGCTKPLVRGVRNASHIHGETGMGNVSYPPEFKTKLDGRHAVQLIIDLIMSHEPKTITLVPTGGLTNIAMAVRLEPRIVDRVKEVVLMGGGYHTGNASPVAEFNVFIDPEAAHIVFNESWNVTMVGLDLTHLALATPAVQKRVREVGTKPAAFMLQILDFYTKVYEKEHDTYGKVHDPCAVAYVIDPTVMTTERVPVDIELNGALTTGMTVADFRYPRPKNCRTQVAVKLDFDKFWCLVIDALERIGDP 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (IUNH_LEIMA | P83851)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0047724    inosine nucleosidase activity    Catalysis of the reaction: inosine + H2O = D-ribose + hypoxanthine.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008477    purine nucleosidase activity    Catalysis of the reaction: a N-D-ribosylpurine + H2O = a purine + D-ribose.
    GO:0045437    uridine nucleosidase activity    Catalysis of the reaction: H(2)O + uridine = ribofuranose + uracil.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a 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).
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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