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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS 7-KETO-8-AMINOPELARGONIC ACID (KAPA) SYNTHASE BIOF
 
Authors :  S. H. Fan, D. F. Li, D. C. Wang, G. J. Chen, X. E. Zhang, L. J. Bi
Date :  20 Aug 14  (Deposition) - 17 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Domain Swapping, Alpha And Beta, Alpha-Beta-Alpha Sandwich, Synthase, Pyridoxal 5'-Phosphate (Plp) Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Fan, D. F. Li, D. C. Wang, J. Fleming, H. T. Zhang, Y. Zhou, L. Zhou, J. Zhou, T. Chen, G. J. Chen, X. E. Zhang, L. J. Bi
Structure And Function Of Mycobacterium Smegmatis 7-Keto-8-Aminopelargonic Acid (Kapa) Synthase
Int. J. Biochem. Cell Biol. V. 58C 71 2014
PubMed-ID: 25462832  |  Reference-DOI: 10.1016/J.BIOCEL.2014.11.006

(-) Compounds

Molecule 1 - 8-AMINO-7-OXONONANOATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.3.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BIOF, MSMEG_3189, MSMEI_3107
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Synonym: AONS, 7-KETO-8-AMINO-PELARGONIC ACID SYNTHASE, 7-KAP SYNTHASE, KAPA SYNTHASE, 8-AMINO-7-KETOPELARGONATE SYNTHASE, ALPHA- OXOAMINE SYNTHASE

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WY7)

(-) Sites  (0, 0)

(no "Site" information available for 3WY7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WY7)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:343 -Pro A:344
2Arg B:29 -Val B:30
3Ala B:130 -Ser B:131
4Pro B:343 -Pro B:344
5Pro C:343 -Pro C:344
6Pro D:343 -Pro D:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WY7)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_2PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site.BIOF_MYCS2232-241
 
 
 		  4A:232-241
B:232-241
C:232-241
D:232-241
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_2PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site.BIOF_MYCS2232-241
 
 
 		  2A:232-241
B:232-241
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_2PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site.BIOF_MYCS2232-241
 
 
 		  2-
-
C:232-241
D:232-241

(-) Exons   (0, 0)

(no "Exon" information available for 3WY7)

(-) 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:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.eeeee...hhhhhhhhhhh....eeeeeee..........hhhhhhhhhhhh..eeeee.............hhhhhh.......eeeeee.........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhh.ee.eee.........eeeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wy7 A  37 ELDLASNDYLGLSQHPDVLDGGVEALRTWGGGAGGSRLVTGNTELHEAFEHQLASFLGAESALVFSSGYTANLGALVALSGPGSLIVSDALSHASLVDACRLSRARVVVSPHRDVDAVDAALAARTEERAVVVTESVFSADGDLAPLRDLHAVCRRHGALLLVDEAHGLGVRGTRGQGLLHEVGLAGAPDIVMTTTLSKALGSQGGAVLGPEAVRAHLIDTARSFIFDTGLAPAAVGAASAALRVLDAEPQRARAVLDRAAELATIAGVTEAPVSAVVSVILGDPEIAVGAAAACLDRGVRVGCFRPPTVPAGTSRLRLAARASLTDDEMALARQVLTDVLATARA 382
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376      


Chain B from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh............ee...........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhh.eeeee...hhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh..eeeee.............hhhhhh.......eeeeee.........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhh.ee.eee.........eeeeee.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wy7 B  12 LADIEQRRRAEGLRRELRVRPPVAAELDLASNDYLGLSQHPDVLDGGVEALRTWGGGAGGSRLVTGNTELHEAFEHQLASFLGAESALVFSSGYTANLGALVALSGPGSLIVSDALSHASLVDACRLSRARVVVSPHRDVDAVDAALAARTEERAVVVTESVFSADGDLAPLRDLHAVCRRHGALLLVDEAHGLGVRGTRGQGLLHEVGLAGAPDIVMTTTLSKALGSQGGAVLGPEAVRAHLIDTARSFIFDTGLAPAAVGAASAALRVLDAEPQRARAVLDRAAELATIAGVTEAPVSAVVSVILGDPEIAVGAAAACLDRGVRVGCFRPPTVPAGTSRLRLAARASLTDDEMALARQVLTDVLATA 380
                                    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       371         


Chain C from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhh.eeeee...hhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh..eeeee.............hhhhhh.......eeeeee.........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhh..ee.eee.....hhhheeeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wy7 C  37 ELDLASNDYLGLSQHPDVLDGGVEALRTWGGGAGGSRLVTGNTELHEAFEHQLASFLGAESALVFSSGYTANLGALVALSGPGSLIVSDALSHASLVDACRLSRARVVVSPHRDVDAVDAALAARTEERAVVVTESVFSADGDLAPLRDLHAVCRRHGALLLVDEAHGLGVRGTRGQGLLHEVGLAGAPDIVMTTTLSKALGSQGGAVLGPEAVRAHLIDTARSFIFDTGLAPAAVGAASAALRVLDAEPQRARAVLDRAAELATIAGVTEAPVSAVVSVILGDPEIAVGAAAACLDRGVRVGCFRPPTVPAGTSRLRLAARASLTDDEMALARQVLTDVLATARA 382
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376      


Chain D from PDB  Type:PROTEIN  Length:371
                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.............ee..........hhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee.hhh..hhhhhhhhh.eeeee...hhhhhhhhhhh.....eeeeee..........hhhhhhhhhhhh..eeeee.............hhhhhh.......eeeeee.........eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhh..eeeee.....hhhheeeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wy7 D  12 LADIEQRRRAEGLRRELRVRPPVAAELDLASNDYLGLSQHPDVLDGGVEALRTWGGGAGGSRLVTGNTELHEAFEHQLASFLGAESALVFSSGYTANLGALVALSGPGSLIVSDALSHASLVDACRLSRARVVVSPHRDVDAVDAALAARTEERAVVVTESVFSADGDLAPLRDLHAVCRRHGALLLVDEAHGLGVRGTRGQGLLHEVGLAGAPDIVMTTTLSKALGSQGGAVLGPEAVRAHLIDTARSFIFDTGLAPAAVGAASAALRVLDAEPQRARAVLDRAAELATIAGVTEAPVSAVVSVILGDPEIAVGAAAACLDRGVRVGCFRPPTVPAGTSRLRLAARASLTDDEMALARQVLTDVLATARA 382
                                    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       371       381
   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  (0, 0)

(no "SCOP Domain" information available for 3WY7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WY7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WY7)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:130 - Ser B:131   [ RasMol ]  
    Arg B:29 - Val B:30   [ RasMol ]  
    Pro A:343 - Pro A:344   [ RasMol ]  
    Pro B:343 - Pro B:344   [ RasMol ]  
    Pro C:343 - Pro C:344   [ RasMol ]  
    Pro D:343 - Pro D:344   [ RasMol ]  
 
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  3wy7
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