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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-CYANOALANINE SYNTHASE IN SOYBEAN
 
Authors :  H. Yi, J. M. Jez
Date :  02 Jan 12  (Deposition) - 12 Sep 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Beta-Cyanoalanine Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yi, M. Juergens, J. M. Jez
Structure Of Soybean Beta-Cyanoalanine Synthase And The Molecular Basis For Cyanide Detoxification In Plants.
Plant Cell V. 24 2696 2012
PubMed-ID: 22739827  |  Reference-DOI: 10.1105/TPC.112.098954

(-) Compounds

Molecule 1 - BETA-CYANOALNINE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.5.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLYMA09G39390, OAS-TL3
    Organism Common: SOYBEANS
    Organism Scientific: GLYCINE MAX
    Organism Taxid: 3847
    Strain: WILLIAMS 82

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:95 , ASN A:126 , MET A:227 , ILE A:229 , GLY A:230 , SER A:231 , GLY A:232 , GLY A:233 , THR A:234 , GLY A:274 , SER A:318 , PRO A:345 , HOH A:604 , HOH A:607BINDING SITE FOR RESIDUE PLP A 500
2AC2SOFTWARELYS B:95 , ASN B:126 , MET B:227 , GLY B:230 , SER B:231 , GLY B:232 , GLY B:233 , THR B:234 , THR B:273 , GLY B:274 , SER B:318 , PRO B:345 , HOH B:603 , HOH B:604BINDING SITE FOR RESIDUE PLP B 501
3AC3SOFTWARELYS C:95 , ASN C:126 , MET C:227 , GLY C:230 , SER C:231 , GLY C:232 , GLY C:233 , THR C:234 , GLY C:274 , SER C:318 , PRO C:345 , HOH C:502 , HOH C:508BINDING SITE FOR RESIDUE PLP C 401
4AC4SOFTWARELYS D:95 , ASN D:126 , MET D:227 , GLY D:228 , GLY D:230 , SER D:231 , GLY D:232 , GLY D:233 , THR D:234 , SER D:318 , PRO D:345 , HOH D:508 , HOH D:514BINDING SITE FOR RESIDUE PLP D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu B:75 -Gly B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VBE)

(-) 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:317
 aligned with I1L6I6_SOYBN | I1L6I6 from UniProtKB/TrEMBL  Length:373

    Alignment length:317
                                    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       
         I1L6I6_SOYBN    51 GTNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENM 367
               SCOP domains d3vbea_ A: automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh....eee..........eeeeee.........hhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.hhhhhhh....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhh..eeeeee..hhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbe A  51 STNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENM 367
                                    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       


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with I1L6I6_SOYBN | I1L6I6 from UniProtKB/TrEMBL  Length:373

    Alignment length:321
                                    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 
         I1L6I6_SOYBN    52 TNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENMQPVAV 372
               SCOP domains d3vbeb_ B: automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh....eee..........eeeeee.........hhhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.hhh........................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh.hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbe B  52 TNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENMQPVAV 372
                                    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:329
 aligned with I1L6I6_SOYBN | I1L6I6 from UniProtKB/TrEMBL  Length:373

    Alignment length:350
                                    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
         I1L6I6_SOYBN    23 LLFSTTTAAIVDSPSLAQRIRDLPKDLPGTNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENMQPVAV 372
               SCOP domains d3vbec_                      C: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........---------------------.....hhhhhh....eee..........eeeeee.hhh.....hhhhhhhhhhhhhhh........eeee...hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhh....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbe C  44 LYFQGHAS---------------------TNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENMQPVAV 372
                                   | -         -        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
                                  51                    52                                                                                                                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:317
 aligned with I1L6I6_SOYBN | I1L6I6 from UniProtKB/TrEMBL  Length:373

    Alignment length:317
                                    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       
         I1L6I6_SOYBN    51 GTNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENM 367
               SCOP domains d3vbed_ D: automated matches                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhh....eee..........eeeeee.........hhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh.....eeeeeee.hhhhhhh....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vbe D  51 STNIKKHVSQLIGRTPLVYLNKVTEGCGAYVAVKQEMMQPTASIKDRPAYAMITDAEEKNLITPGKTTLIEPTSGNMGISMAFMAAMKGYKMVLTMPSYTSLERRVTMRAFGAELILTDPAKGMGGTVKKAYELLENTPNAHMLQQFSNPANTQVHFETTGPEIWEDTNGQVDIFVMGIGSGGTVSGVGQYLKSKNPNVKIYGVEPSESNVLNGGKPGPHHITGNGVGFKPDILDLDVMEKVLEVSSEDAVNMARVLALKEGLMVGISSGANTVAALRLAQLPENKGKLIVTVHPSFGERYLSSVLFQELRQEAENM 367
                                    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
   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 3VBE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (I1L6I6_SOYBN | I1L6I6)
molecular function
    GO:0050017    L-3-cyanoalanine synthase activity    Catalysis of the reaction: L-cysteine + HCN = sulfide + L-3-cyanoalanine.
    GO:0004124    cysteine synthase activity    Catalysis of the reaction: O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019499    cyanide metabolic process    The chemical reactions and pathways involving cyanide, NC-, the anion of hydrocyanic acid. Cyanide is a potent inhibitor of respiration, reacting with the ferric form of cytochrome aa3 and thus blocking the electron transport chain.
    GO:0019344    cysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0006535    cysteine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of cysteine from other compounds, including serine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

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        I1L6I6_SOYBN | I1L6I6: 3vc3

(-) Related Entries Specified in the PDB File

3vc3