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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE NIT3, A MEMBER OF BRANCH 10 OF THE NITRILASE SUPERFAMILY
 
Authors :  D. Kumaran, S. Eswaramoorthy, F. W. Studier, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  29 Jun 00  (Deposition) - 04 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitrilase, Dimer, Structural Genomics, Four Layer Sandwich, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, S. Eswaramoorthy, S. E. Gerchman, H. Kycia, F. W. Studier, S. Swaminathan
Crystal Structure Of A Putative Cn Hydrolase From Yeast
Proteins V. 52 283 2003
PubMed-ID: 12833551  |  Reference-DOI: 10.1002/PROT.10417
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 32.5 KDA PROTEIN YLR351C
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: YLR351C, L9638.5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1F89)

(-) Sites  (0, 0)

(no "Site" information available for 1F89)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F89)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F89)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F89)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CN_HYDROLASEPS50263 Carbon-nitrogen hydrolase domain profile.NIT3_YEAST11-264
 		  2A:11-264
B:311-564
2UPF0012PS01227 Uncharacterized protein family UPF0012 signature.NIT3_YEAST165-185
 		  2A:165-185
B:465-485

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR351C1YLR351C.1XII:830363-829488876NIT3_YEAST1-2912912A:2-282 (gaps)
B:302-582 (gaps)		281
281

(-) 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:271
 aligned with NIT3_YEAST | P49954 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:281
                                    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 
           NIT3_YEAST     2 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHLFDVDIPNGISFHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPELAMLSARKGAFAMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGKIVAEAGEGEEIIYAELDPEVIESFRQAVPLTKQRRF 282
               SCOP domains d1f89a_ A: hypothetical protein yl85                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1f89A00 A:2-282  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhh........hhhhhhhhhhhhhh..eee...eeee......eeeeeeee.....eeeeee....----------hhhhhh.......eeeee..eeeee.hhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeee................eee.....eeee.....eeeeeeehhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CN_HYDROLASE  PDB: A:11-264 UniProt: 11-264                                                                                                                                                                                                                   ------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------UPF0012              ------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:2-282 (gaps) UniProt: 1-291 [INCOMPLETE]                                                                                                                                                                                                                                 Transcript 1
                 1f89 A   2 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHL----------FHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPELAMLSARKGAFAMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGKIVAEAGEGEEIIYAELDPEVIESFRQAVPLTKQRRF 282
                                    11        21        31        41        51        61        71        81        91       101       111       121       131         -|      151       161       171       181       191       201       211       221       231       241       251       261       271       281 
                                                                                                                                                           131        142                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:271
 aligned with NIT3_YEAST | P49954 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:281
                                    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 
           NIT3_YEAST     2 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHLFDVDIPNGISFHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPELAMLSARKGAFAMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGKIVAEAGEGEEIIYAELDPEVIESFRQAVPLTKQRRF 282
               SCOP domains d1f89b_ B: hypothetical protein yl85                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1f89B00 B:302-582  [code=3.60.110.10, no name defined]                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhh........hhhhhhhhhhhhhh..eee...eeee......eeeeeeee.....eeeeee....----------hhhhh........eeeee..eeeee.hhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhh.eeeee................eee.....eeee.....eeeeeeehhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CN_HYDROLASE  PDB: B:311-564 UniProt: 11-264                                                                                                                                                                                                                  ------------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------UPF0012              ------------------------------------------------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:302-582 (gaps) UniProt: 1-291 [INCOMPLETE]                                                                                                                                                                                                                               Transcript 1
                 1f89 B 302 SASKILSQKIKVALVQLSGSSPDKMANLQRAATFIERAMKEQPDTKLVVLPECFNSPYSTDQFRKYSEVINPKEPSTSVQFLSNLANKFKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHRKVHL----------FHESETLSPGEKSTTIDTKYGKFGVGICYDMRFPELAMLSARKGAFAMIYPSAFNTVTGPLHWHLLARSRAVDNQVYVMLCSPARNLQSSYHAYGHSIVVDPRGKIVAEAGEGEEIIYAELDPEVIESFRQAVPLTKQRRF 582
                                   311       321       331       341       351       361       371       381       391       401       411       421       431         -|      451       461       471       481       491       501       511       521       531       541       551       561       571       581 
                                                                                                                                                           431        442
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F89)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NIT3_YEAST | P49954)
molecular function
    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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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  1f89
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 Related Entries

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