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(-) Description

Title :  CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE FROM STREPTOCOCCUS THERMOPHILUS
 
Authors :  K. Hernandez, I. Zelen, G. Petrillo, I. Uson, C. Wandtke, J. Bujons, J. J T. Parella, P. Clapes
Date :  13 Nov 14  (Deposition) - 04 Feb 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Aldolase, Serine Hydrodymethyltransferase, Transferase, Aldehydes, Catalysis, Catalytic Domain, Escherichia Coli, Chemical, Protein Binding, Protein Conformation, Protein Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hernandez, I. Zelen, G. Petrillo, I. Uson, C. M. Wandtke, J. Bujons, J. Joglar, T. Parella, P. Clapes
Engineered L-Serine Hydroxymethyltransferase From Streptococcus Thermophilus For The Synthesis Of Alpha , Alpha-Dialkyl-Alpha-Amino Acids.
Angew. Chem. Int. Ed. Engl. V. 54 3013 2015
PubMed-ID: 25611820  |  Reference-DOI: 10.1002/ANIE.201411484

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GLYA, STR0755
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 299768
    Strain: CNRZ 1066
    Synonym: SERINE METHYLASE

 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  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2CIT4Ligand/IonCITRIC ACID
3GOL4Ligand/IonGLYCEROL
4NA3Ligand/IonSODIUM ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2CIT2Ligand/IonCITRIC ACID
3GOL2Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2CIT2Ligand/IonCITRIC ACID
3GOL2Ligand/IonGLYCEROL
4NA-1Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:91 , GLY A:92 , SER A:93 , THR A:221 , HIS A:223 , LYS A:224 , ARG A:230 , CAC A:502 , HOH A:669 , HOH A:673 , HOH A:787 , TYR C:49 , HIS C:90 , GLN C:254 , GLY C:255binding site for residue CIT A 501
02AC2SOFTWARESER A:29 , LEU A:121 , HIS A:198 , LYS A:224 , ARG A:357 , CIT A:501 , TYR C:59binding site for residue CAC A 502
03AC3SOFTWARETYR A:53 , ILE A:73 , ALA A:85 , ASN A:86 , ASN A:246 , HOH A:776 , HOH A:777 , HOH A:778binding site for residue GOL A 503
04AC4SOFTWARESER B:91 , GLY B:92 , SER B:93 , THR B:221 , HIS B:223 , LYS B:224 , ARG B:230 , TYR D:49 , HIS D:90 , GLN D:254 , GLY D:255binding site for residue CIT B 501
05AC5SOFTWARESER B:29 , HIS B:198 , LYS B:224 , ARG B:357 , TYR D:59binding site for residue CAC B 502
06AC6SOFTWAREPHE B:295 , ASN B:296 , HIS B:298 , PHE B:301binding site for residue NA B 503
07AC7SOFTWARETYR B:53 , LYS B:56 , ILE B:73 , ALA B:85 , ASN B:86 , ASN B:246 , HOH B:681 , HOH B:719 , HOH B:728binding site for residue GOL B 504
08AC8SOFTWARETYR A:49 , HIS A:90 , GLN A:254 , GLY A:255 , SER C:91 , GLY C:92 , SER C:93 , HIS C:223 , LYS C:224 , ARG C:230 , CAC C:502 , HOH C:642 , HOH C:739binding site for residue CIT C 501
09AC9SOFTWARETYR A:59 , SER C:29 , HIS C:198 , LYS C:224 , ARG C:357 , CIT C:501binding site for residue CAC C 502
10AD1SOFTWAREPHE C:295 , ASN C:296 , HIS C:298 , PHE C:301binding site for residue NA C 503
11AD2SOFTWARETYR C:53 , ALA C:85 , ASN C:86 , ASN C:246 , HOH C:757 , HOH C:762binding site for residue GOL C 504
12AD3SOFTWARETYR B:49 , HIS B:90 , GLN B:254 , GLY B:255 , SER D:91 , GLY D:92 , SER D:93 , THR D:221 , HIS D:223 , LYS D:224 , ARG D:230 , HOH D:640binding site for residue CIT D 501
13AD4SOFTWARETYR B:49 , SER D:29 , HIS D:198 , LYS D:224 , ARG D:357binding site for residue CAC D 502
14AD5SOFTWAREPHE D:295 , ASN D:296 , HIS D:298 , PHE D:301binding site for residue NA D 503
15AD6SOFTWAREILE D:73 , ALA D:85 , ASN D:86 , ASN D:246 , HOH D:642 , HOH D:666binding site for residue GOL D 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:250 -Pro A:251
2Phe B:250 -Pro B:251
3Phe C:250 -Pro C:251
4Phe D:250 -Pro D:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WXB)

(-) 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:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.....................eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee......hhhhhhhhhhhh.ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxb A   1 DYKAFDPELWNAIDAEAERQQNNIELIASENVVSKAVMAAQGTLLTNKYAEGYPGKRYYGGTAVIDVVETLAIERAKKLFGAKFANVQPHSGSQANAAVYMSLIQPGDTVMGMDLSAGGHLTHGAPVSFSGKTYNFVSYNVDKESELLDYDAILAQAKEVRPKLIVAGASAYSRIIDFAKFREIADAVGAYLMVDMAHIAGLVASGHHPSPVPYAHVTTTTTHKTLRGPRGGLILTDDEDIAKKLNSAVFPGLQGGPLEHVIAAKAVALKEALDPAFKEYGENVIKNAAAMADVFNQHPDFRVISGGTNNHLFLVDVTKVVENGKVAQNVLEEVNITLNKNSIPYEQLSPFKTSGIRVGSPAITSRGMGEAESRQIAEWMVEALENHDKPEVLERIRGDVKVLTDAFPLY 410
                                    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


Chain B from PDB  Type:PROTEIN  Length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee...hhhhhhh.eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhh...........eeeee..........eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee......hhhhhhhhhhhh.ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxb B   1 DYKAFDPELWNAIDAEAERQQNNIELIASENVVSKAVMAAQGTLLTNKYAEGYPGKRYYGGTAVIDVVETLAIERAKKLFGAKFANVQPHSGSQANAAVYMSLIQPGDTVMGMDLPVSFSGKTYNFVSYNVDKESELLDYDAILAQAKEVRPKLIVAGASAYSRIIDFAKFREIADAVGAYLMVDMAHIAGLVASGHHPSPVPYAHVTTTTTHKTLRGPRGGLILTDDEDIAKKLNSAVFPGLQGGPLEHVIAAKAVALKEALDPAFKEYGENVIKNAAAMADVFNQHPDFRVISGGTNNHLFLVDVTKVVENGKVAQNVLEEVNITLNKNSIPYEQLSPFKTSGIRVGSPAITSRGMGEAESRQIAEWMVEALENHDKPEVLERIRGDVKVLTDAFPLY 410
                                    10        20        30        40        50        60        70        80        90       100       110    || 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
                                                                                                                                            115|                                                                                                                                                                                                                                                                                            
                                                                                                                                             126                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee...hhhhhhh.eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee..........eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee......hhhhhhhhhhhh.ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxb C   1 DYKAFDPELWNAIDAEAERQQNNIELIASENVVSKAVMAAQGTLLTNKYAEGYPGKRYYGGTAVIDVVETLAIERAKKLFGAKFANVQPHSGSQANAAVYMSLIQPGDTVMGMDLPVSFSGKTYNFVSYNVDKESELLDYDAILAQAKEVRPKLIVAGASAYSRIIDFAKFREIADAVGAYLMVDMAHIAGLVASGHHPSPVPYAHVTTTTTHKTLRGPRGGLILTDDEDIAKKLNSAVFPGLQGGPLEHVIAAKAVALKEALDPAFKEYGENVIKNAAAMADVFNQHPDFRVISGGTNNHLFLVDVTKVVENGKVAQNVLEEVNITLNKNSIPYEQLSPFKTSGIRVGSPAITSRGMGEAESRQIAEWMVEALENHDKPEVLERIRGDVKVLTDAFPLY 410
                                    10        20        30        40        50        60        70        80        90       100       110    || 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
                                                                                                                                            115|                                                                                                                                                                                                                                                                                            
                                                                                                                                             126                                                                                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.ee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee.....................eeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhh..eeeee...hhhhhhhh..........eeeee.hhhhh....eeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee......hhhhhhhhhhh..ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wxb D   1 DYKAFDPELWNAIDAEAERQQNNIELIASENVVSKAVMAAQGTLLTNKYAEGYPGKRYYGGTAVIDVVETLAIERAKKLFGAKFANVQPHSGSQANAAVYMSLIQPGDTVMGMDLSAGGHLTHGAPVSFSGKTYNFVSYNVDKESELLDYDAILAQAKEVRPKLIVAGASAYSRIIDFAKFREIADAVGAYLMVDMAHIAGLVASGHHPSPVPYAHVTTTTTHKTLRGPRGGLILTDDEDIAKKLNSAVFPGLQGGPLEHVIAAKAVALKEALDPAFKEYGENVIKNAAAMADVFNQHPDFRVISGGTNNHLFLVDVTKVVENGKVAQNVLEEVNITLNKNSIPYEQLSPFKTSGIRVGSPAITSRGMGEAESRQIAEWMVEALENHDKPEVLERIRGDVKVLTDAFPLY 410
                                    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
   Legend:   → Mismatch (orange background)
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  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 4WXB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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        GLYA_STRT1 | Q5M0B4: 4wxf 4wxg

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