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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTATE BETA-SEMIALDEHIDE DEHYDROGENASE FROM STREPTOCOCCUS PNEUMONIAE WITH D-2,3-DIAMINOPROPIONATE
 
Authors :  A. G. Pavlovsky, X. Liu, C. R. Faehnle, N. Potente, R. E. Viola
Date :  13 Dec 10  (Deposition) - 04 Jan 12  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nadp, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Pavlovsky, X. Liu, C. R. Faehnle, N. Potente, R. E. Viola
Structural Characterization Of Inhibitors With Selectivity Against Members Of A Homologous Enzyme Family.
Chem. Biol. Drug Des. V. 79 128 2012
PubMed-ID: 22039970  |  Reference-DOI: 10.1111/J.1747-0285.2011.01267.X

(-) Compounds

Molecule 1 - ASPARTATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.2.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGSSP23BS72_03388
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406563
    Strain: SP23-BS72

 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
12RA3Ligand/Ion3-AMINO-D-ALANINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
12RA2Ligand/Ion3-AMINO-D-ALANINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12RA1Ligand/Ion3-AMINO-D-ALANINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:127 , CYS A:128 , GLN A:155 , GLY A:159 , GLU A:220 , ARG A:245BINDING SITE FOR RESIDUE 2RA A 367
2AC2SOFTWAREASN B:127 , CYS B:128 , GLN B:155 , GLY B:159 , ALA B:160 , GLU B:220 , ARG B:245BINDING SITE FOR RESIDUE 2RA B 367
3AC3SOFTWAREASN C:127 , CYS C:128 , GLN C:155 , GLY C:159 , ILE C:209 , GLU C:220 , ARG C:245BINDING SITE FOR RESIDUE 2RA C 367

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:190 -Pro A:191
2Leu B:190 -Pro B:191
3Leu C:190 -Pro C:191
4Leu D:190 -Pro D:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PYL)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d3pyla1 A:2-127,A:330-359 Aspartate beta-semialdehyde dehydrogenase                                                           d3pyla2 A:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3pyla1 A:2-127,A:330-359      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeeeeeee.......eeee..eeee.ee..........eeee..hhhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeeeeee......eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pyl A   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFELKL 359
                                    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       321       331       341       351        


Chain B from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d3pylb1 B:2-127,B:330-355 Aspartate beta-semialdehyde dehydrogenase                                                           d3pylb2 B:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3pylb1 B:2-127,B:330-355  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeeeeeee.......eeee..eeee.ee..........eeee..hhhhhhhhhhhhhhhh.eeee..............hhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeeeeee......eeeeeeee.....hhhhhhhhhhh...eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pyl B   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKF 355
                                    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       321       331       341       351    


Chain C from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d3pylc1 C:2-127,C:330-362 Aspartate beta-semialdehyde dehydrogenase                                                           d3pylc2 C:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3pylc1 C:2-127,C:330-362         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh....eeeeeeee.......eeee..eeee.ee..........eeee..hhhhhhhhhhhhhhhh.eeee..............hhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeeeeee......eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pyl C   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFELKLEHH 362
                                    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       321       331       341       351       361 


Chain D from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d3pyld1 D:2-127,D:330-357 Aspartate beta-semialdehyde dehydrogenase                                                           d3pyld2 D:128-329 Aspartate beta-semialdehyde dehydrogenase                                                                                                                                               d3pyld1 D:2-127,D:330-357    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhh....eeeeeeee.......eeee..eeee.ee.hhhhh....eeee..hhhhhhhhhhhhhhh..eeee..............hhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhh................................hhhhhhhhhhhhhhh.....eeeeeeee......eeeeeeee.....hhhhhhhhhhhh..eee..hhhhh...hhhhhh....eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pyl D   2 GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQDITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQNPDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIVSTYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPIAFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSAHSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRDTFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVRPTAELKFEL 357
                                    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       321       331       341       351
   Legend:   → Mismatch (orange background)
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    → 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  (2, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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(-) Related Entries Specified in the PDB File

3pwk CRYSTAL STRUCTURE OF ASPARTATE BETA-SEMIALDEHIDE DEHYDROGENASE FROM STREPTOCOCCUS PNEUMONIAE WITH 2',5'- ADENOSINE DIPHOSPHATE AND CYCLOHEXANE-1,4-DICARBOXYLATE
3pws CRYSTAL STRUCTURE OF ASPARTATE BETA-SEMIALDEHIDE DEHYDROGENASE FROM STREPTOCOCCUS PNEUMONIAE WITH 2',5'- ADENOSINE DIPHOSPHATE AND D-2-AMINOADIPATE
3pyx
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3q0e
3q11
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