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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 :  1.84
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
1JJJ4Mod. Amino AcidS-(PYRIDIN-3-YLCARBONYL)-L-CYSTEINE
2ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:53 , HIS A:55 , GLU A:64 , HIS A:71 , JJJ A:136 , HOH A:205BINDING SITE FOR RESIDUE ZN A 192
2AC2SOFTWAREASP B:53 , HIS B:55 , GLU B:64 , HIS B:71 , JJJ B:136 , HOH B:260BINDING SITE FOR RESIDUE ZN B 192
3AC3SOFTWAREASP C:53 , HIS C:55 , GLU C:64 , HIS C:71 , JJJ C:136 , HOH C:229BINDING SITE FOR RESIDUE ZN C 192
4AC4SOFTWAREASP D:53 , HIS D:55 , GLU D:64 , HIS D:71 , JJJ D:136 , HOH D:266BINDING SITE FOR RESIDUE ZN D 192

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O93)

(-) 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 3O93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O93)

(-) Exons   (0, 0)

(no "Exon" information available for 3O93)

(-) 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: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 d3o93a_ A: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o93 A   1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDIcVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     | 140       150       160       170       180       190
                                                                                                                                                                 136-JJJ                                                  


Chain B from PDB  Type:PROTEIN  Length:189
 aligned with A0A0H2UR34_S | A0A0H2UR34 from UniProtKB/TrEMBL  Length:191

    Alignment length:189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
         A0A0H2UR34_S     2 TKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDICVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
               SCOP domains d3o93b_ 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
                 3o93 B   2 TKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDIcVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    |  141       151       161       171       181         
                                                                                                                                                                136-JJJ                                                  


Chain C from PDB  Type:PROTEIN  Length:188
 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 d3o93c_ C: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeee...--...hhhhhh........hhhhh..hhhhhhhhhhh....eeeeee.........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh...eee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o93 C   1 MTKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHE--DCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDIcVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    10        20        30        40        50     |  60        70        80        90       100       110       120       130     | 140       150       160       170       180       190
                                                                                  56 59                                                                          136-JJJ                                                  


Chain D from PDB  Type:PROTEIN  Length:187
 aligned with A0A0H2UR34_S | A0A0H2UR34 from UniProtKB/TrEMBL  Length:191

    Alignment length:189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
         A0A0H2UR34_S     2 TKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHEENDCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDICVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
               SCOP domains d3o93d_ 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
                 3o93 D   2 TKALISIDYTEDFVADSGKLTAGAPAQAISDAISKVTRLAFERGDYIFFTIDAHE--DCFHPESKLFPPHNLIGTSGRNLYGDLGIFYQEHGSDSRVFWMDKRHYSAFSGTDLDIRLRERRVSTVILTGVLTDIcVLHTAIDAYNLGYDIEIVKPAVASIWPENHQFALGHFKNTLGAKLVDENLNELF 190
                                    11        21        31        41        51    |  |61        71        81        91       101       111       121       131    |  141       151       161       171       181         
                                                                                 56 59                                                                          136-JJJ
   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 3O93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O93)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3O93)

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

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  A0A0H2UR34_S | A0A0H2UR34
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 Related Entries

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

UniProtKB/TrEMBL
        A0A0H2UR34_S | A0A0H2UR34: 3o90 3o91 3o92 3o94

(-) Related Entries Specified in the PDB File

3o90 3o91 3o92 3o94