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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURES OF STREPTOCOCCUS PNEUMONIAE NICOTINAMIDASE WITH TRAPPED INTERMEDIATES PROVIDE INSIGHTS INTO CATALYTIC MECHANISM AND INHIBITION BY ALDEHYDES
 
Authors :  J. B. French, Y. Cen, A. A. Sauve, S. E. Ealick
Date :  03 Aug 10  (Deposition) - 12 Jan 11  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nicotinamidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. French, Y. Cen, A. A. Sauve, S. E. Ealick
High-Resolution Crystal Structures Of Streptococcus Pneumoniae Nicotinamidase With Trapped Intermediates Provid Insights Into The Catalytic Mechanism And Inhibition By Aldehydes .
Biochemistry V. 49 8803 2010
PubMed-ID: 20853856  |  Reference-DOI: 10.1021/BI1012436

(-) Compounds

Molecule 1 - NICOTINAMIDASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SP_1583
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: ISOCHORISMATASE FAMILY PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NCA4Ligand/IonNICOTINAMIDE
2ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , PHE A:14 , LEU A:21 , ASP A:53 , GLU A:64 , PHE A:68 , HIS A:71 , TYR A:106 , VAL A:131 , LEU A:132 , ILE A:135 , SER A:136 , ZN A:193BINDING SITE FOR RESIDUE NCA A 192
2AC2SOFTWAREASP A:53 , HIS A:55 , GLU A:64 , HIS A:71 , NCA A:192 , HOH A:204BINDING SITE FOR RESIDUE ZN A 193
3AC3SOFTWAREASP B:9 , PHE B:14 , ASP B:53 , GLU B:64 , PHE B:68 , HIS B:71 , TYR B:106 , VAL B:131 , LEU B:132 , ILE B:135 , SER B:136 , ZN B:193 , HOH B:201BINDING SITE FOR RESIDUE NCA B 192
4AC4SOFTWAREASP B:53 , HIS B:55 , GLU B:64 , HIS B:71 , NCA B:192 , HOH B:201BINDING SITE FOR RESIDUE ZN B 193
5AC5SOFTWAREASP C:9 , PHE C:14 , ASP C:53 , GLU C:64 , HIS C:71 , TYR C:106 , VAL C:131 , LEU C:132 , ILE C:135 , SER C:136 , ZN C:193BINDING SITE FOR RESIDUE NCA C 192
6AC6SOFTWAREASP C:53 , HIS C:55 , GLU C:64 , HIS C:71 , NCA C:192 , HOH C:515BINDING SITE FOR RESIDUE ZN C 193
7AC7SOFTWAREASP D:9 , PHE D:14 , ASP D:53 , GLU D:64 , PHE D:68 , HIS D:71 , TYR D:106 , VAL D:131 , LEU D:132 , ILE D:135 , SER D:136 , ZN D:193BINDING SITE FOR RESIDUE NCA D 192
8AC8SOFTWAREASP D:53 , HIS D:55 , GLU D:64 , HIS D:71 , NCA D:192 , HOH D:233BINDING SITE FOR RESIDUE ZN D 193

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O94)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:131 -Leu A:132
2Val B:131 -Leu B:132
3Val C:131 -Leu C:132
4Val D:131 -Leu D:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O94)

(-) Exons   (0, 0)

(no "Exon" information available for 3O94)

(-) 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:189
 aligned with A0A0H2UR34_S | A0A0H2UR34 from UniProtKB/TrEMBL  Length:191

    Alignment length:189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
         A0A0H2UR34_S     1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDICVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNEL 189
               SCOP domains d3o94a_ A: automated matches                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o94 A   1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDISVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNEL 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:190
 aligned with A0A0H2UR34_S | A0A0H2UR34 from UniProtKB/TrEMBL  Length:191

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         A0A0H2UR34_S     1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDICVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
               SCOP domains d3o94b_ B: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o94 B   1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDISVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain C from PDB  Type:PROTEIN  Length:190
 aligned with A0A0H2UR34_S | A0A0H2UR34 from UniProtKB/TrEMBL  Length:191

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         A0A0H2UR34_S     1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDICVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
               SCOP domains d3o94c_ C: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o94 C   1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDISVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain D from PDB  Type:PROTEIN  Length:190
 aligned with A0A0H2UR34_S | A0A0H2UR34 from UniProtKB/TrEMBL  Length:191

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
         A0A0H2UR34_S     1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDICVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
               SCOP domains d3o94d_ D: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o94 D   1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDISVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (0, 0)

(no "CATH Domain" information available for 3O94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O94)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3O94)

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  Cis Peptide Bonds
    Val A:131 - Leu A:132   [ RasMol ]  
    Val B:131 - Leu B:132   [ RasMol ]  
    Val C:131 - Leu C:132   [ RasMol ]  
    Val D:131 - Leu D:132   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2UR34_S | A0A0H2UR34: 3o90 3o91 3o92 3o93

(-) Related Entries Specified in the PDB File

3o90 3o91 3o92 3o93