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(-) Description

Title :  CRYSTAL STRUCTURE OF Y60ABSSHMT L-SER EXTERNAL ALDIMINE
 
Authors :  V. Rajaram, V. R. Pai, S. Bisht, B. S. Bhavani, N. Appaji Rao, H. S. Savithri, M. R. N. Murthy
Date :  29 Jan 08  (Deposition) - 16 Dec 08  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Plp-Dependent Enzymes, Y60A, Transferase, Folate Binding, Pyridoxal Phosphate, One-Carbon Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. R. Pai, V. Rajaram, S. Bisht, B. S. Bhavani, N. A. Rao, M. R. N. Murthy, H. S. Savithri
Structural And Functional Studies Of Bacillus Stearothermophilus Serine Hydroxymethyltransferase: The Role Of Asn(341), Tyr(60) And Phe(351) In Tetrahydrofolate Binding.
Biochem. J. V. 418 635 2009
PubMed-ID: 19046138  |  Reference-DOI: 10.1042/BJ20081739

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PRSET C
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-405
    Mutation: YES
    Organism Scientific: BACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: SCHIFF LINKAGE BETWEEN PLP B 501 AND SER B 502
    Synonym: SHMT, SERINE METHYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3PO41Ligand/IonPHOSPHATE ION
4SER1Mod. Amino AcidSERINE
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3PO42Ligand/IonPHOSPHATE ION
4SER2Mod. Amino AcidSERINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:51 , SER A:93 , GLY A:94 , ALA A:95 , HIS A:122 , ALA A:171 , SER A:172 , ASP A:197 , ALA A:199 , HIS A:200 , THR A:223 , HIS A:225 , LYS A:226 , GLY A:256 , GLY A:257 , SER A:502 , HOH A:2258 , HOH A:2389 , HOH A:2390BINDING SITE FOR RESIDUE PLP A 501
2AC2SOFTWARESER A:31 , GLU A:53 , TYR A:61 , HIS A:122 , HIS A:200 , LYS A:226 , ARG A:357 , PLP A:501 , HOH A:2391BINDING SITE FOR RESIDUE SER A 502
3AC3SOFTWARETYR A:152 , ARG A:156 , ILE A:186 , LEU A:322 , VAL A:387 , HOH A:2215 , HOH A:2218 , HOH A:2312BINDING SITE FOR RESIDUE MPD A 701
4AC4SOFTWAREGLU A:371 , GLU A:375 , HOH A:2356 , HOH A:2392 , HOH A:2393BINDING SITE FOR RESIDUE PO4 A 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VMT)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:251 -Pro A:252

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VMT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VMT)

(-) Exons   (0, 0)

(no "Exon" information available for 2VMT)

(-) 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:406
 aligned with Q7SIB6_GEOSE | Q7SIB6 from UniProtKB/TrEMBL  Length:419

    Alignment length:407
                                    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       
         Q7SIB6_GEOSE     1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRYYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTDPT 407
               SCOP domains d2vmta_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2vmtA01 A:1-32,A:284-405        2vmtA02 A:33-283 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                       2vmtA01 A:1-32,A:284-405 Aspartate Aminotransferase, domain 1                                                             -- CATH domains
               Pfam domains ---SHMT-2vmtA01 A:4-380                                                                                                                                                                                                                                                                                                                                                                     --------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhh....eeeee......hhhhh...hhhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh...........eeeee..........eeeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee.............eeeeehhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vmt A   1 MKYLPQQDPQVFAAIEQERKRQHAKIELIASENFVSRAVMEAQGSVLTNKYAEGYPGRRAYGGCEYVDIVEELARERAKQLFGAEHANVQPHSGAQANMAVYFTVLEHGDTVLGMNLSHGGHLTHGSPVNFSGVQYNFVAYGVDPETHVIDYDDVREKARLHRPKLIVAAASAYPRIIDFAKFREIADEVGAYLMVDMAHIAGLVAAGLHPNPVPYAHFVTTTTHKTLRGPRGGMILCQEQFAKQIDKAIFPGIQGGPLMHVIAAKAVAFGEALQDDFKAYAKRVVDNAKRLASALQNEGFTLVSGGTDNHLLLVDLRPQQLTGKTAEKVLDEVGITVNKNTIPYDPESPFVTSGIRIGTAAVTTRGFGLEEMDEIAAIIGLVLKNVGSEQALEEARQRVAALTD-S 502
                                    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    | |
                                                                                                                                                                                                                                                                                                                                                                                                                                              405 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                502
   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, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7SIB6_GEOSE | Q7SIB6)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004372    glycine hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
    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:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    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:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0019264    glycine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7SIB6_GEOSE | Q7SIB6: 1kkj 1kkp 1kl1 1kl2 1yjs 1yjy 1yjz 2vgs 2vgt 2vgu 2vgv 2vgw 2vi8 2vi9 2via 2vib 2vmn 2vmo 2vmp 2vmq 2vmr 2vms 2vmu 2vmv 2vmw 2vmx 2vmy 2vmz 2w7d 2w7e 2w7f 2w7g 2w7h 2w7i 2w7j 2w7k 2w7l 2w7m

(-) Related Entries Specified in the PDB File

1kkj CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASE FROMB.STEAROTHERMOPHILUS
1kkp CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH SERINE
1kl1 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH GLYCINE
1kl2 CRYSTAL STRUCTURE OF SERINE HYDROXYMETHYLTRANSFERASECOMPLEXED WITH GLYCINE AND 5-FORMYL TETRAHYDROFOLATE
1yjs K226Q MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B.STEAROTHERMOPHILUS, COMPLEX WITH GLYCINE
1yjy K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B.STEAROTHERMOPHILUS, COMPLEX WITH SERINE
1yjz K226M MUTANT OF SERINE HYDROXYMETHYLTRANSFERASE FROM B.STEAROTHERMOPHILUS
2vgs CRYSTAL STRUCTURE OF E53QBSSHMT INTERNAL ALDIMINE
2vgt CRYSTAL STRUCTURE OF E53QBSSHMT WITH GLYCINE
2vgu CRYSTAL STRUCTURE OF E53QBSSHMT WITH L-SERINE
2vgv CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF L-ALLO-THREONINE
2vgw CRYSTAL STRUCTURE OF E53QBSSHMT OBTAINED IN THE PRESENCE OF GLYCINE AND 5-FOMYL TETRAHYDROFOLATE
2vi8 CRYSTAL STRUCTURE OF S172ABSSHMT INTERNAL ALDIMINE
2vi9 CRYSTAL STRUCTURE OF S172ABSSHMT GLYCINE EXTERNAL ALDIMINE
2via CRYSTAL STRUCTURE OF S172ABSSHMT L-SERINE EXTERNAL ALDIMINE
2vib CRYSTAL STRUCTURE OF S172ABSSHMT OBTAINED IN THE PRESENCE OF L-ALLO-THR
2vmn CRYSTAL STRUCTURE OF N341ABSSHMT INTERNAL ALDIMINE
2vmo CRYSTAL STRUCTURE OF N341ABSSHMT GLY EXTERNAL ALDIMINE
2vmp CRYSTAL STRUCTURE OF N341ABSSHMT L-SER EXTERNAL ALDIMINE
2vmq STRUCTURE OF N341ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L-ALLO-THR
2vmr CRYSTAL STRUCTURE OF Y60ABSSHMT INTERNAL ALDIMINE
2vms CRYSTAL STRUCTURE OF Y60ABSSHMT CRYSTALLIZED IN THE PRESENCE OF GLYCINE
2vmu CRYSTAL STRUCTURE OF Y60ABSSHMT CRYSTALLIZED IN THE PRESENCE OF L-ALLO-THR
2vmv CRYSTAL STRUCTURE OF F351GBSSHMT INTERNAL ALDIMINE
2vmw CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH L-SER
2vmx CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH L-ALLO-THR
2vmy CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH GLY AND FTHF
2vmz CRYSTAL STRUCTURE OF F351GBSSHMT IN COMPLEX WITH GLY