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(-) Description

Title :  CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS IN COMPLEX WITH THE PLP EXTERNAL ALDIMINE ADDUCT WITH KANOSAMINE-6-PHOSPHATE
 
Authors :  K. E. Van Straaten, D. R. J. Palmer, D. A. R. Sanders
Date :  09 Apr 13  (Deposition) - 16 Oct 13  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sugar Aminotransferase, Aspertate Aminotransferase Fold, Homo-Dimer, Additional N-Terninal Domain, 3-Keto-Glucose-6-Phosphate Aminitransferase, Kanosamine-6-Phosphate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Van Straaten, J. B. Ko, R. Jagdhane, S. Anjum, D. R. Palmer, D. A. Sanders
The Structure Of Ntda, A Sugar Aminotransferase Involved In The Kanosamine Biosynthetic Pathway In Bacillus Subtilis, Reveals A New Subclass Of Aminotransferases.
J. Biol. Chem. V. 288 34121 2013
PubMed-ID: 24097983  |  Reference-DOI: 10.1074/JBC.M113.500637

(-) Compounds

Molecule 1 - NTD BIOSYNTHESIS OPERON PROTEIN NTDA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21-GOLD (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 939788, BSU10550, NP_388936.1, NTDA, YHJL
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3O1G2Ligand/Ion3-DEOXY-3-[(E)-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE)AMINO]-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:124 , GLY A:125 , THR A:126 , SER A:150 , PHE A:151 , ALA A:153 , THR A:154 , ASP A:222 , CYS A:224 , GLN A:225 , SER A:242 , ASN A:244 , TYR A:246 , LYS A:247 , TYR A:379 , HOH A:630 , HOH A:652 , HOH A:657 , HOH A:666 , HOH A:719 , HOH A:781 , THR B:98 , SER B:99 , TYR B:274 , LYS B:282 , ASN B:292 , HOH B:726BINDING SITE FOR RESIDUE O1G A 501
02AC2SOFTWAREGLN A:173 , PHE A:175 , GLU A:338 , LEU A:339 , PRO A:340 , PRO A:352 , LYS A:354 , HOH A:650 , HOH A:815BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREASP A:376 , VAL A:377 , TYR A:378 , ASN B:283 , HOH B:1036BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWARETYR A:246 , ARG A:317 , HIS A:349 , LEU A:415BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREASN A:149 , PHE A:175 , TYR A:199 , LEU A:382 , HIS A:407 , VAL A:410 , HOH A:611BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREGLN A:2 , GLU A:29 , HOH A:952BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWARETHR A:98 , SER A:99 , TYR A:274 , LYS A:282 , ASN A:292 , SER B:124 , GLY B:125 , THR B:126 , SER B:150 , PHE B:151 , ALA B:153 , THR B:154 , ASP B:222 , CYS B:224 , GLN B:225 , SER B:242 , ASN B:244 , TYR B:246 , LYS B:247 , TYR B:379 , HOH B:630 , HOH B:631 , HOH B:638 , HOH B:676 , HOH B:702 , HOH B:708 , HOH B:728 , HOH B:873BINDING SITE FOR RESIDUE O1G B 501
08AC8SOFTWAREASN A:283 , ASP B:376 , VAL B:377 , TYR B:378 , HOH B:768BINDING SITE FOR RESIDUE EDO B 502
09AC9SOFTWAREILE B:166 , TYR B:167 , TYR B:395 , LEU B:398BINDING SITE FOR RESIDUE ACT B 503
10BC1SOFTWARETYR B:246 , ARG B:317 , HIS B:349 , LEU B:415 , HOH B:610BINDING SITE FOR RESIDUE ACT B 504
11BC2SOFTWAREASN B:149 , PHE B:175 , LEU B:198 , TYR B:199 , LEU B:382 , HIS B:407 , VAL B:410 , HOH B:613BINDING SITE FOR RESIDUE EDO B 505
12BC3SOFTWAREGLN B:173 , PHE B:175 , GLU B:338 , PRO B:340 , PRO B:352 , LYS B:354 , HOH B:654 , HOH B:898BINDING SITE FOR RESIDUE EDO B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K2M)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:378 -Tyr A:379
2Tyr B:378 -Tyr B:379

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K2M)

(-) Exons   (0, 0)

(no "Exon" information available for 4K2M)

(-) 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:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..hhhhhhhhhhhhhh......eee..hhhhhhhhhhh....hhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeee.....hhhhhhhhhhh.eeee..........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhhh.eeeee...............eeeee.............eeeee.hhhhhhhhhhhhh.....................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh................eeee....hhhhhhhhhhhhhh.........hhhhh.hhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2m A  -1 AGMQKQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEKIDIEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFTSGPYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPANSFSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHLYGKHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYKNFGVCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEIG 440
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438  


Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhh......eeee..hhhhhhhhhhh....hhhhhh...............hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeee.....hhhhhhhhhh..eeee..........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhh..eeeee...............eeeee.............eeeee.hhhhhhhhhhhhh.....................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh................eeee....hhhhhhhhhhhhhh.........hhhhh.hhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2m B   1 MQKQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEKIDIEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFTSGPYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPANSFSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHLYGKHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYKNFGVCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQEI 439
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430
   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 4K2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K2M)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:378 - Tyr A:379   [ RasMol ]  
    Tyr B:378 - Tyr B:379   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        NTDA_BACSU | O07566: 4k2b 4k2i

(-) Related Entries Specified in the PDB File

4k2b CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS IN COMPLEX WITH THE INTERNAL ALDIMINE
4k2i CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS WITH BOUND COFACTOR PMP