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(-) Description

Title :  CRYSTAL STRUCTURE OF PNC1 FROM L. INFANTUM IN COMPLEX WITH NICOTINATE
 
Authors :  E. Gazanion, D. Garcia, J. -F. Guichou, G. Labesse, D. Sereno, B. Vergne
Date :  14 Mar 11  (Deposition) - 24 Aug 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha/Beta-Hydrolase-Like, Nicotinamidase, Cytoplasmic, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Gazanion, D. Garcia, R. Silvestre, C. Gerard, J. F. Guichou, G. Labesse, M. Seveno, A. Cordeiro-Da-Silva, A. Ouaissi, D. Sereno, B. Vergnes
The Leishmania Nicotinamidase Is Essential For Nad(+) Production And Parasite Proliferation.
Mol. Microbiol. V. 82 21 2011
PubMed-ID: 21819459  |  Reference-DOI: 10.1111/J.1365-2958.2011.07799.X

(-) Compounds

Molecule 1 - ALPHA/BETA-HYDROLASE-LIKE PROTEIN
    Chains: A, B, C, D
    EC Number: 3.5.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-45B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LINJ01.0460
    Organism Scientific: LEISHMANIA INFANTUM
    Organism Taxid: 5671

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2NIO4Ligand/IonNICOTINIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NIO2Ligand/IonNICOTINIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NIO2Ligand/IonNICOTINIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:73 , HIS A:75 , HIS A:92 , NIO A:311BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREASP A:32 , LEU A:44 , ASP A:73 , TRP A:89 , HIS A:92 , LYS A:117 , ALA A:157 , PHE A:160 , CYS A:161 , ZN A:301BINDING SITE FOR RESIDUE NIO A 311
03AC3SOFTWAREASP B:73 , HIS B:75 , HIS B:92 , NIO B:311BINDING SITE FOR RESIDUE ZN B 301
04AC4SOFTWAREASP B:32 , LEU B:44 , ASP B:73 , TRP B:89 , HIS B:92 , LYS B:117 , TYR B:126 , ALA B:157 , PHE B:160 , CYS B:161 , ZN B:301BINDING SITE FOR RESIDUE NIO B 311
05AC5SOFTWAREARG B:150BINDING SITE FOR RESIDUE CL B 321
06AC6SOFTWAREASP C:73 , HIS C:75 , HIS C:92 , ASP C:124 , NIO C:311BINDING SITE FOR RESIDUE ZN C 301
07AC7SOFTWAREASP C:32 , ASP C:73 , TRP C:89 , HIS C:92 , LYS C:117 , ALA C:157 , PHE C:160 , CYS C:161 , ZN C:301BINDING SITE FOR RESIDUE NIO C 311
08AC8SOFTWAREASP D:73 , HIS D:75 , HIS D:92 , NIO D:311BINDING SITE FOR RESIDUE ZN D 301
09AC9SOFTWAREASP D:32 , PHE D:37 , ASP D:73 , TRP D:89 , HIS D:92 , LYS D:117 , ALA D:157 , PHE D:160 , CYS D:161 , ZN D:301BINDING SITE FOR RESIDUE NIO D 311
10BC1SOFTWARETHR D:20BINDING SITE FOR RESIDUE CL D 321

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R2J)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Val A:156 -Ala A:157
2Val B:156 -Ala B:157
3Pro C:40 -Gly C:41
4Gly C:41 -Gly C:42
5Val C:156 -Ala C:157
6Val D:156 -Ala D:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R2J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R2J)

(-) Exons   (0, 0)

(no "Exon" information available for 3R2J)

(-) 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:199
 aligned with A4HRG8_LEIIN | A4HRG8 from UniProtKB/TrEMBL  Length:218

    Alignment length:199
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
         A4HRG8_LEIIN    16 TLCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
               SCOP domains d3r2ja_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee..hhhhhh.........hhhhhhhhhhhhhhh...eeeeeee........hhhhh..........hhhhh...........eeeee....................hhhhhhhhhh..eeeeee....hhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhh...eeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2j A  16 TLCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with A4HRG8_LEIIN | A4HRG8 from UniProtKB/TrEMBL  Length:218

    Alignment length:200
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214
         A4HRG8_LEIIN    15 PTLCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
               SCOP domains d3r2jb_ B: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....eeeeee..hhhhhh...........hhhhhhhhhhhhh...eeeeeee........hhhhh..........hhhhh.....hhhhh.eeeee....................hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh..eeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2j B  15 PTLCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214


Chain C from PDB  Type:PROTEIN  Length:198
 aligned with A4HRG8_LEIIN | A4HRG8 from UniProtKB/TrEMBL  Length:218

    Alignment length:198
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        
         A4HRG8_LEIIN    17 LCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
               SCOP domains d3r2jc_ C: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.....eeeeee..hhhhhh........hhhhhhhhhhhhhhhh...eeeeeee........hhhhh..........................eeeee....................hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhh...eeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r2j C  17 LCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        


Chain D from PDB  Type:PROTEIN  Length:199
 aligned with A4HRG8_LEIIN | A4HRG8 from UniProtKB/TrEMBL  Length:218

    Alignment length:199
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205         
         A4HRG8_LEIIN    16 TLCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
               SCOP domains d3r2jd_ D: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeeeee..hhhhhh.........hhhhhhhhhhhhhhh...eeeeeee........hhhhh..........hhhhh.....hhhhh.eeeee....................hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhh..eeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2j D  16 TLCVTVSSTTDVLIIADMQVDFLAPGGSLHVKGGEALLDGINAVSSQLPFRYQVATQDWHPENHCSFVTHGGPWPPHCVQGSAGAQLHAGLHTQRINAVIRKGVTQQADSYSAFVEDNGVSTGLAGLLHSIGARRVFVCGVAYDFCVFFTAMDARKNGFSVVLLEDLTAAVDDAAWSARTAELKDAGVVLLKSSALVAE 214
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R2J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R2J)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A4HRG8_LEIIN | A4HRG8)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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