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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE 1 FROM GEOBACILLUS KAUSTOPHILUS
 
Authors :  M. Kanagawa, S. Baba, N. Nakagawa, A. Ebihara, S. Kuramitsu, S. Yokoyam G. Sampei, G. Kawai, Riken Structural Genomics/Proteomics Initi (Rsgi)
Date :  18 Feb 11  (Deposition) - 07 Mar 12  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rossmann Fold, Transformylase, Folate Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Sampei, M. Kanagawa, S. Baba, T. Shimasaki, H. Taka, S. Mitsui, S. Fujiwara, Y. Yanagida, M. Kusano, S. Suzuki, K. Terao, H. Kawai, Y. Fukai, N. Nakagawa, A. Ebihara, S. Kuramitsu, S. Yokoyama, G. Kawai
Structures And Reaction Mechanisms Of The Two Related Enzymes, Purn And Puru.
J. Biochem. V. 154 569 2013
PubMed-ID: 24108189  |  Reference-DOI: 10.1093/JB/MVT090

(-) Compounds

Molecule 1 - PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    Chains: A
    EC Number: 2.1.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-HISTEV
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GK0266
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:231 , HOH A:234 , HOH A:340 , HOH A:379 , HOH A:435 , HOH A:439BINDING SITE FOR RESIDUE MG A 211
2AC2SOFTWAREHOH A:279 , HOH A:351 , HOH A:357 , HOH A:454 , HOH A:457 , HOH A:480BINDING SITE FOR RESIDUE MG A 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AV3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:113 -Pro A:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AV3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AV3)

(-) Exons   (0, 0)

(no "Exon" information available for 3AV3)

(-) Sequences/Alignments

Asymmetric/Biological 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    
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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:188
 aligned with Q5L3C9_GEOKA | Q5L3C9 from UniProtKB/TrEMBL  Length:210

    Alignment length:188
                             1                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        
         Q5L3C9_GEOKA     - -MKRLAVFASGSGTNFQAIVDAAKRGDLPARVALLVCDRPGAKVIERAARENVPAFVFSPKDYPSKAAFESEILRELKGRQIDWIALAGYMRLIGPTLLSAYEGKIVNIHPSLLPAFPGKDAIGQAYRAGVSETGVTVHYVDEGMDTGPVIAQRVVPIVPGEPIEALEERIHQVEHELYPTVLRMLLG 187
               SCOP domains d3av3a_ A: automated matches                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3av3 A   0 HmKRLAVFASGSGTNFQAIVDAAKRGDLPARVALLVCDRPGAKVIERAARENVPAFVFSPKDYPSKAAFESEILRELKGRQIDWIALAGYmRLIGPTLLSAYEGKIVNIHPSLLPAFPGKDAIGQAYRAGVSETGVTVHYVDEGmDTGPVIAQRVVPIVPGEPIEALEERIHQVEHELYPTVLRmLLG 187
                             |       9        19        29        39        49        59        69        79        89|       99       109       119       129       139    |  149       159       169       179    |   
                             |                                                                                       90-MSE                                               144-MSE                                 184-MSE
                             1-MSE
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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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AV3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AV3)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5L3C9_GEOKA | Q5L3C9)
molecular function
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0004644    phosphoribosylglycinamide formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
    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:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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