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(-) Description

Title :  CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE WITH COVALENTLY BOUND PLP SCHIFF-BASE FROM PLASMODIUM FALCIPARUM
 
Authors :  P. Chitnumsub, A. Jaruwat, U. Leartsakulpanich
Date :  24 Dec 13  (Deposition) - 11 Jun 14  (Release) - 11 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha/Beta Protein, Transferase, Methyltransferase Activity, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Chitnumsub, W. Ittarat, A. Jaruwat, K. Noytanom, W. Amornwatcharapong, W. Pornthanakasem, P. Chaiyen, Y. Yuthavong, U. Leartsakulpanich
The Structure Of Plasmodium Falciparum Serine Hydroxymethyltransferase Reveals A Novel Redox Switch That Regulates Its Activities
Acta Crystallogr. , Sect. D V. 70 1517 2014
PubMed: search  |  Reference-DOI: 10.1107/S1399004714005598

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET100/D
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PFL1720W, SHMT1
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PLP3Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:100 , GLY A:101 , SER A:102 , HIS A:129 , ASP A:208 , SER A:210 , HIS A:211 , THR A:234 , HIS A:236 , LYS A:237 , HOH A:832 , TYR B:54 , GLY B:272BINDING SITE FOR RESIDUE PLP A 701
2AC2SOFTWARETYR A:54 , GLY A:272 , SER B:100 , GLY B:101 , SER B:102 , HIS B:129 , THR B:183 , ASP B:208 , SER B:210 , HIS B:211 , THR B:234 , HIS B:236 , LYS B:237 , HOH B:832BINDING SITE FOR RESIDUE PLP B 701
3AC3SOFTWARESER C:100 , GLY C:101 , SER C:102 , HIS C:129 , THR C:183 , ASP C:208 , SER C:210 , HIS C:211 , THR C:234 , HIS C:236 , LYS C:237 , TYR D:54 , GLY D:271 , GLY D:272BINDING SITE FOR RESIDUE PLP C 701
4AC4SOFTWARETYR C:54 , GLY C:271 , GLY C:272 , SER D:100 , GLY D:101 , SER D:102 , THR D:234BINDING SITE FOR RESIDUE PO4 D 501

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:125 -A:364

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:266 -Pro A:267
2Phe B:266 -Pro B:267
3Phe C:266 -Pro C:267
4Phe D:266 -Pro D:267

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O6Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O6Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4O6Z)

(-) 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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh...eeeee......hhhhh........hhhhhh.eeeee........hhhhhhhhhhhh...eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6z A  -5 HPFTPGMFNNDPLQKYDKELFDLLEKEKNRQIETINLIASENLTNTAVRECLGDRISNKYSEGYPHKRYYGGNDYVDKIEELCYKRALEAFNVSEEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDLFESKLYKCNSEGYVDMESVRNLALSFQPKVIICGYTSYPRDIDYKGFREICDEVNAYLFADISHISSFVACNLLNNPFTYADVVTTTTHKILRGPRSALIFFNKKRNPGIDQKINSSVFPSFQGGPHNNKIAAVACQLKEVNTPEFKEYTKQVLLNSKALAECLLKRNLDLVTNGTDNHLIVVDLRKYNITGSKLQETCNAINIALNKNTIPSDVDCVSPSGIRIGTPALTTRGCKEKDMEFIADMLLKAILLTDELQQKYGKKLVDFKKGLVNNPKIDELKKEVVQWAKNLPFA 442
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434        


Chain B from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh...eeeee.hhhh.hhhhh........hhhhhhheeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhh...eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6z B  -2 TPGMFNNDPLQKYDKELFDLLEKEKNRQIETINLIASENLTNTAVRECLGDRISNKYSEGYPHKRYYGGNDYVDKIEELCYKRALEAFNVSEEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDLFESKLYKCNSEGYVDMESVRNLALSFQPKVIICGYTSYPRDIDYKGFREICDEVNAYLFADISHISSFVACNLLNNPFTYADVVTTTTHKILRGPRSALIFFNKKRNPGIDQKINSSVFPSFQGGPHNNKIAAVACQLKEVNTPEFKEYTKQVLLNSKALAECLLKRNLDLVTNGTDNHLIVVDLRKYNITGSKLQETCNAINIALNKNTIPSDVDCVSPSGIRIGTPALTTRGCKEKDMEFIADMLLKAILLTDELQQKYGKKLVDFKKGLVNNPKIDELKKEVVQWAKNLPFA 442
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437     


Chain C from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh...eeeee......hhhhh........hhhhhh.eeeee........hhhhhhhhhhhh...eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6z C   2 FNNDPLQKYDKELFDLLEKEKNRQIETINLIASENLTNTAVRECLGDRISNKYSEGYPHKRYYGGNDYVDKIEELCYKRALEAFNVSEEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDLFESKLYKCNSEGYVDMESVRNLALSFQPKVIICGYTSYPRDIDYKGFREICDEVNAYLFADISHISSFVACNLLNNPFTYADVVTTTTHKILRGPRSALIFFNKKRNPGIDQKINSSVFPSFQGGPHNNKIAAVACQLKEVNTPEFKEYTKQVLLNSKALAECLLKRNLDLVTNGTDNHLIVVDLRKYNITGSKLQETCNAINIALNKNTIPSDVDCVSPSGIRIGTPALTTRGCKEKDMEFIADMLLKAILLTDELQQKYGKKLVDFKKGLVNNPKIDELKKEVVQWAKNLPFA 442
                                    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       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441 


Chain D from PDB  Type:PROTEIN  Length:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhhh...eeeee.hhhh.hhhhh........hhhhhhheeeee........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhh...eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o6z D  -2 TPGMFNNDPLQKYDKELFDLLEKEKNRQIETINLIASENLTNTAVRECLGDRISNKYSEGYPHKRYYGGNDYVDKIEELCYKRALEAFNVSEEEWGVNVQPLSGSAANVQALYALVGVKGKIMGMHLCSGGHLTHGFFDEKKKVSITSDLFESKLYKCNSEGYVDMESVRNLALSFQPKVIICGYTSYPRDIDYKGFREICDEVNAYLFADISHISSFVACNLLNNPFTYADVVTTTTHKILRGPRSALIFFNKKRNPGIDQKINSSVFPSFQGGPHNNKIAAVACQLKEVNTPEFKEYTKQVLLNSKALAECLLKRNLDLVTNGTDNHLIVVDLRKYNITGSKLQETCNAINIALNKNTIPSDVDCVSPSGIRIGTPALTTRGCKEKDMEFIADMLLKAILLTDELQQKYGKKLVDFKKGLVNNPKIDELKKEVVQWAKNLPFA 442
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
   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 4O6Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O6Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O6Z)

(-) Gene Ontology  (10, 10)

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