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(-) Description

Title :  CRYSTAL STRUCTURE OF YWFH, NADPH DEPENDENT REDUCTASE INVOLVED IN BACILYSIN BIOSYNTHESIS
 
Authors :  M. Rajavel, B. Gopal
Date :  07 Oct 11  (Deposition) - 06 Mar 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Nadph Binding Motif, Rossmann Fold, Short Chain Dehydrogenase, Reductase, Sdr Super Family, Oxidoreductase, Bacilysin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Rajavel, K. Perinbam, B. Gopal
Structural Insights Into The Role Of Bacillus Subtilis Ywfh (Bacg) In Tetrahydrotyrosine Synthesis
Acta Crystallogr. , Sect. D V. 69 324 2013
PubMed-ID: 23519407  |  Reference-DOI: 10.1107/S0907444912046690

(-) Compounds

Molecule 1 - BACILYSIN BIOSYNTHESIS OXIDOREDUCTASE YWFH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSU37680, IPA-86R, YWFH
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3U49)

(-) Sites  (0, 0)

(no "Site" information available for 3U49)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U49)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U49)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U49)

(-) Exons   (0, 0)

(no "Exon" information available for 3U49)

(-) 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:249
 aligned with BACG_BACSU | P39644 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:259
                                                                                                                                                                                                                                                                                           259 
                                    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       | 
           BACG_BACSU     2 SKRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSISKQKAEEQIASGIPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKSI-   -
               SCOP domains d3u49a_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh----------...ee...hhhhhhhhhhhhhhhhhh.....eee......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u49 A   2 SKRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSIS----------GIPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKSIL 260
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    |    -     | 221       231       241       251         
                                                                                                                                                                                                                                      206        217                                           


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with BACG_BACSU | P39644 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:259
                                                                                                                                                                                                                                                                                          259  
                                    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      |  
           BACG_BACSU     3 KRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSISKQKAEEQIASGIPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKSI--   -
               SCOP domains d3u49b_ B: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh......eee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhhh..--------..ee...hhhhhhhhhhhhhhhhhh.....eee......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u49 B   3 KRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSISKQK--------IPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKSILE 261
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |  -     | 222       232       242       252         
                                                                                                                                                                                                                                        209      218                                           


Chain C from PDB  Type:PROTEIN  Length:252
 aligned with BACG_BACSU | P39644 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:257
                                    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       
           BACG_BACSU     2 SKRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSISKQKAEEQIASGIPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKS 258
               SCOP domains d3u49c_ C: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh......-----.........hhhhhhhhhhhhhhhhhh.....eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u49 C   2 SKRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSISKQKA-----SGIPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKS 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201        |-    |  221       231       241       251       
                                                                                                                                                                                                                                          210   216                                          


Chain D from PDB  Type:PROTEIN  Length:242
 aligned with BACG_BACSU | P39644 from UniProtKB/Swiss-Prot  Length:259

    Alignment length:257
                                    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       
           BACG_BACSU     2 SKRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNSISKQKAEEQIASGIPMKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKS 258
               SCOP domains d3u49d_ D: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh---------------.....hhhhhhhhhhhhhhhhhh.....eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u49 D   2 SKRTAFVMGASQGIGKAIALKLADQHFSLVINSRNLDNIESVKEDILAKHPEASVIVLAGDMSDQHTRAGIFQKIESQCGRLDVLINNIPGGAPDTFDNCNIEDMTATFTQKTVAYIDAIKRASSLMKQNEFGRIINIVGNLWKEPGANMFTNSMMNAALINASKNISIQLAPHNITVNCLNPGFIATDRYHQFVENVMKKNS---------------MKRVGSAEETAALAAFLASEEASYITGQQISADGGSMKS 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201  |      -       221       231       241       251       
                                                                                                                                                                                                                                    204             220
   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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U49)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BACG_BACSU | P39644)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016628    oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  3u49
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 Related Entries

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

UniProtKB/Swiss-Prot
        BACG_BACSU | P39644: 3u4c 3u4d

(-) Related Entries Specified in the PDB File

3u4c 3u4d