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(-) Description

Title :  CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS WITH BOUND COFACTOR PMP
 
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 :  2.23
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sugar Aminotransferase, Aspertate Aminotransferase Fold, Homo-Dimer, Additional N-Terninal Domain, 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: 511693
    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  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:124 , GLY A:125 , THR A:126 , SER A:150 , PHE A:151 , ALA A:153 , ASP A:222 , CYS A:224 , GLN A:225 , SER A:242 , ASN A:244 , LYS A:247 , ALA A:255 , TYR A:379 , ACT A:509 , HOH A:620 , HOH A:622 , HOH A:686 , HOH A:770 , HOH A:856 , ASN B:292BINDING SITE FOR RESIDUE PMP A 501
02AC2SOFTWARETYR A:246 , ARG A:317 , HIS A:349 , LEU A:415 , ACT A:508BINDING SITE FOR RESIDUE ACT A 502
03AC3SOFTWAREASP A:376 , VAL A:377 , TYR A:378 , LYS B:282 , ASN B:283BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREVAL A:119 , HOH A:786BINDING SITE FOR RESIDUE CL A 504
05AC5SOFTWAREASN A:149 , PHE A:175 , TYR A:199 , LEU A:382 , HIS A:407 , VAL A:410 , HOH A:607BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREGLN A:173 , PHE A:175 , LEU A:339 , PRO A:340 , PRO A:352 , LYS A:354 , HOH A:681BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREILE A:381 , LEU A:382 , MET A:385 , HIS A:407BINDING SITE FOR RESIDUE CL A 507
08AC8SOFTWARETYR A:246 , LYS A:247 , HIS A:349 , TYR A:378 , ACT A:502BINDING SITE FOR RESIDUE ACT A 508
09AC9SOFTWARETYR A:246 , PMP A:501 , HOH A:622 , HOH A:856 , HOH A:875 , TYR B:274BINDING SITE FOR RESIDUE ACT A 509
10BC1SOFTWAREGLY A:95 , LYS A:96 , PHE A:97 , THR A:98 , SER A:99 , PRO B:245 , TYR B:246BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREASN A:292 , HOH A:647 , SER B:124 , GLY B:125 , THR B:126 , SER B:150 , ALA B:153 , ASP B:222 , CYS B:224 , GLN B:225 , SER B:242 , ASN B:244 , LYS B:247 , ALA B:255 , TYR B:379 , HOH B:632 , HOH B:710 , HOH B:744 , HOH B:805BINDING SITE FOR RESIDUE PMP B 501
12BC3SOFTWAREGLN B:173 , PHE B:175 , GLU B:338 , PRO B:340 , PRO B:352 , HOH B:704 , HOH B:875BINDING SITE FOR RESIDUE EDO B 502
13BC4SOFTWARETYR B:246 , ARG B:317 , HIS B:349 , LEU B:415BINDING SITE FOR RESIDUE ACT B 503
14BC5SOFTWAREASN B:149 , PHE B:175 , TYR B:199 , LEU B:382 , HIS B:407 , VAL B:410 , HOH B:605BINDING SITE FOR RESIDUE EDO B 504
15BC6SOFTWARELYS A:282 , ASN A:283 , ASP B:376 , VAL B:377 , TYR B:378BINDING SITE FOR RESIDUE EDO B 505
16BC7SOFTWARETYR B:118 , VAL B:119 , HOH B:837BINDING SITE FOR RESIDUE CL B 506
17BC8SOFTWARELEU B:382 , MET B:385 , HIS B:407BINDING SITE FOR RESIDUE CL B 507
18BC9SOFTWAREPRO A:245 , TYR A:246 , GLY B:95 , LYS B:96 , PHE B:97 , THR B:98 , SER B:99BINDING SITE FOR RESIDUE EDO B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K2I)

(-) 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 4K2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K2I)

(-) Exons   (0, 0)

(no "Exon" information available for 4K2I)

(-) 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:435
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhh......eeee..hhhhhhhhhh.....hhhhhh...............hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeee.....hhhhhhhhhh..eeee..........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhh..eeeee...............eeeee.............eeeee.hhhhhhhhhhhhh.....................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh................eeee.hhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2i A   3 KQVKISGKSKENMSLLKHLKGDVQGKELVIEDSIVNERWKQVLKEKIDIEHDLFNYQKNREISKVPFLPVDRLITNDEVEDILNTLTEVLPTGKFTSGPYLEQFEKVLSTYLHKRYVIATSSGTDAIMIGLLALGLNPGDEVIMPANSFSATENAVLASGGVPIYVDINPQTFCIDPDKIEEAITPYTKFILPVHLYGKHSDMQHIRQIANRYKLKVIEDACQGIGLTDLGKYADITTLSFNPYKNFGVCGKAGAIATDNEELAKKCIQFSYHGFEVNVKNKKVINFGFNSKMDNLQAAIGLERMKYLSLNNFKRLFLADRYITQLAELQNKGYIELPELSEDHVWHLFPIKVRTEDRADIMTKLNEDFGVQTDVYYPILSHMQKTPLVQDKYAGLQLVHTEKAHSQVLHLPLYPSFTLEEQDRVMEGLFHVIKQ 437
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432     


Chain B from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..hhhhhhhhhhhhhh......eee..hhhhhhhhhhh....hhhhhh...............hhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh......eeee.....hhhhhhhhhh..eeee..........hhhhhhhhh...eeee...hhhhh..hhhhhhhhhhhhh.eeeee...............eeeee.............eeeee.hhhhhhhhhhhhh.....................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh................eeee.hhhhhhhhhhhhhhhhh.........hhhhh.hhhhhhhh....hhhhhhhhhheeee......hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k2i 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 4K2I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K2I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K2I)

(-) 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 4k2m

(-) Related Entries Specified in the PDB File

4k2b CRYSTAL STRUCTURE OF NTDA FROM BACILLUS SUBTILIS IN COMPLEX WITH THE INTERNAL ALDIMINE
4k2m