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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMO SAPIENS HOLO SERINE HYDROXYMETHYLTRANSFERASE 2 (MITOCHONDRIAL) (SHMT2), ISOFORM 3, TRANSCRIPT VARIANT 5, 483 AA, AT 2.6 ANG. RESOLUTION
 
Authors :  G. Giardina, P. Brunotti, A. Fiascarelli, R. Contestabile, F. Cutruzz
Date :  17 Mar 14  (Deposition) - 28 Jan 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydroxymethyltransferase, Aat-Like Fold, One Carbon Metabolism, Transferase, 5-Formyl-Thf, Methylase, Mitochondrial (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Giardina, P. Brunotti, A. Fiascarelli, A. Cicalini, M. G. Costa, A. M. Buckle, M. L. Di Salvo, A. Giorgi, M. Marani, A. Paone, S. Rinaldo A. Paiardini, R. Contestabile, F. Cutruzzola
How Pyridoxal 5'-Phosphate Differentially Regulates Human Cytosolic And Mitochondrial Serine Hydroxymethyltransferase Oligomeric State.
Febs J. V. 282 1225 2015
PubMed-ID: 25619277  |  Reference-DOI: 10.1111/FEBS.13211

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 2.1.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SHMT2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SHMT, GLYCINE HYDROXYMETHYLTRANSFERASE, SERINE METHYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2LLP2Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:55 , HIS A:150 , HIS A:233 , LLP A:259 , ARG A:404 , TYR B:75 , GLU B:77 , TYR B:85 , HOH B:628BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWAREARG A:209 , LEU A:210 , ILE A:211 , TYR A:213 , ILE A:234 , PRO A:244 , ASN A:358BINDING SITE FOR RESIDUE PEG A 502
3AC3SOFTWARETYR A:75 , GLU A:77 , TYR A:85 , SER B:55 , HIS B:233 , LLP B:259 , ARG B:404BINDING SITE FOR RESIDUE GOL B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:299 -Pro A:300
2Phe B:299 -Pro B:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PVF)

(-) 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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh.........hhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pvf A  22 WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHkTLRGARSGLIFYRKGVKAIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH 483
                                    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     ||289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479    
                                                                                                                                                                                                                                                                       259-LLP           277|                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                          286                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhh...ee..ee....hhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh....eeeee.hhhh.hhhhh.........hhhhhheeeee.........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh....hhhhh..eeeee.hhhhh....eeeeee........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.hhh....eeeee......hhhhhhhhhhhh.ee.eee.....eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pvf B  22 WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHkTLRGARSGLIFYRKGVKAIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCTPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH 483
                                    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     ||289       299       309       319       329       339       349       359       369       379       389 ||    406       416       426       436       446       456       466       476       
                                                                                                                                                                                                                                                                       259-LLP           277|                                                                                                      391|                                                                                    
                                                                                                                                                                                                                                                                                          286                                                                                                       399
   Legend:   → Mismatch (orange background)
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  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 4PVF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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        GLYM_HUMAN | P34897: 3ou5

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