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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE BETA-ASPARTATE METHYLTRANSFERASE (PCMT) FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
 
Authors :  A. K. Wernimont, A. Hassanali, L. Lin, J. Lew, Y. Zhao, M. Ravichandran, M. Vedadi, I. Kozieradzki, A. Bochkarev, A. M. Edwards, C. H. Arrowsmi J. Weigelt, M. Sundstrom, R. Hui, W. Qiu, Structural Genomics Conso (Sgc)
Date :  28 Mar 07  (Deposition) - 10 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Methyltransferase, Protein Repair, Isoaspartyl Formation, P. Falciparum, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, A. Hassanali, L. Lin, J. Lew, Y. Zhao, M. Ravichandran G. Wasney, M. Vedadi, I. Kozieradzki, A. Bochkarev, A. M. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, R. Hui, W. Qiu
Crystal Structure Of A Putative Protein-L-Isoaspartate O-Methyltransferase Beta-Aspartate Methyltransferase (Pcmt) From Plasmodium Falciparum In Complex With S-Adenosyl-L-Homocysteine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE BETA-ASPARTATE METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.77
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-LIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 15-240
    Gene: PF14_0309
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:59 , THR A:60 , ILE A:61 , SER A:62 , HIS A:67 , GLY A:88 , SER A:89 , GLY A:90 , SER A:91 , GLU A:116 , ARG A:117 , VAL A:118 , LYS A:147 , ASN A:148 , ILE A:149 , GLY A:169 , VAL A:222 , SER A:223 , LEU A:224 , LYS A:225 , HOH A:305 , HOH A:315 , HOH A:319 , HOH A:379BINDING SITE FOR RESIDUE SAH A 301
2AC2SOFTWAREVAL B:59 , THR B:60 , ILE B:61 , SER B:62 , HIS B:67 , GLY B:88 , SER B:89 , GLY B:90 , SER B:91 , GLU B:116 , ARG B:117 , VAL B:118 , LYS B:147 , ASN B:148 , ILE B:149 , GLY B:169 , VAL B:222 , SER B:223 , LEU B:224 , LYS B:225 , HOH B:307 , HOH B:317 , HOH B:321 , HOH B:379BINDING SITE FOR RESIDUE SAH B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PBF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PBF)

(-) 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:218
 aligned with Q8ILD5_PLAF7 | Q8ILD5 from UniProtKB/TrEMBL  Length:240

    Alignment length:219
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
         Q8ILD5_PLAF7    22 ENNHKSLLENLKRRGIIDDDDVYNTMLQVDRGKYIKEIPYIDTPVYISHGVTISAPHMHALSLKRLINVLKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLERVKDLVNFSLENIKRDKPELLKIDNFKIIHKNIYQVNEEEKKELGLFDAIHVGASASELPEILVDLLAENGKLIIPIEEDYTQVLYEITKKNGKIIKDRLFDVCFVSLKKN 240
               SCOP domains d2pbfa_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains 2pbfA00 A:9-227 Vaccinia Virus protein VP39                                                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........eeee..eee.hhhhhhhhhhhhh.......eeeee....hhhhhhhhhhh........eeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeeeee..eeeeeeee....-.eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbf A   9 ENNHKSLLENLKRRGIIDDDDVYNTMLQVDRGKYIKEIPYIDTPVYISHGVTISAPHMHALSLKRLINVLKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLERVKDLVNFSLENIKRDKPELLKIDNFKIIHKNIYQVNEEEKKELGLFDAIHVGASASELPEILVDLLAENGKLIIPIEEDYTQVLYEITKKNG-IIKDRLFDVCFVSLKKN 227
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208| |    218         
                                                                                                                                                                                                                                  209 |                
                                                                                                                                                                                                                                    211                


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q8ILD5_PLAF7 | Q8ILD5 from UniProtKB/TrEMBL  Length:240

    Alignment length:219
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
         Q8ILD5_PLAF7    22 ENNHKSLLENLKRRGIIDDDDVYNTMLQVDRGKYIKEIPYIDTPVYISHGVTISAPHMHALSLKRLINVLKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLERVKDLVNFSLENIKRDKPELLKIDNFKIIHKNIYQVNEEEKKELGLFDAIHVGASASELPEILVDLLAENGKLIIPIEEDYTQVLYEITKKNGKIIKDRLFDVCFVSLKKN 240
               SCOP domains d2pbfb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains 2pbfB00 B:9-227 Vaccinia Virus protein VP39                                                                                                                                                                                 CATH domains
           Pfam domains (1) -PCMT-2pbfB01 B:10-227                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) -PCMT-2pbfB02 B:10-227                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........eeee..eee.hhhhhhhhhhhhh.......eeeee....hhhhhhhhhhh........eeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh.eeeeee.......hhhhhhheeeeeeeeeeeee..eeeeeeee....-.eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbf B   9 ENNHKSLLENLKRRGIIDDDDVYNTMLQVDRGKYIKEIPYIDTPVYISHGVTISAPHMHALSLKRLINVLKPGSRAIDVGSGSGYLTVCMAIKMNVLENKNSYVIGLERVKDLVNFSLENIKRDKPELLKIDNFKIIHKNIYQVNEEEKKELGLFDAIHVGASASELPEILVDLLAENGKLIIPIEEDYTQVLYEITKKNG-IIKDRLFDVCFVSLKKN 227
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208| |    218         
                                                                                                                                                                                                                                  209 |                
                                                                                                                                                                                                                                    211
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ILD5_PLAF7 | Q8ILD5)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004719    protein-L-isoaspartate (D-aspartate) O-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-beta-aspartate = S-adenosyl-L-homocysteine + protein L-beta-aspartate methyl ester.
    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:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0030091    protein repair    The process of restoring a protein to its original state after damage by such things as oxidation or spontaneous decomposition of residues.

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