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(-) Description

Title :  CRYSTAL STRUCTURE OF GAR TRANSFORMYLASE FROM AQUIFEX AEOLICUS
 
Authors :  M. Kanagawa, S. Baba, S. Kuramitsu, S. Yokoyama, G. Kawai, G. Sampei, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Apr 07  (Deposition) - 23 Oct 07  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Rossmann Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, 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-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2MG1Ligand/IonMAGNESIUM ION
3MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2MG-1Ligand/IonMAGNESIUM ION
3MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:13 , ASN A:14 , HOH A:911BINDING SITE FOR RESIDUE MG A 703
2AC2SOFTWAREHIS A:109 , ASP A:145 , HOH A:774BINDING SITE FOR RESIDUE CO A 704
3AC3SOFTWARELYS A:131 , VAL A:157 , LEU A:158 , PRO A:159 , HOH A:768 , HOH A:929BINDING SITE FOR RESIDUE CO A 727
4AC4SOFTWAREGLU A:53 , LYS A:79 , HIS A:120 , HOH A:909 , HOH A:973 , HOH A:1004 , HOH A:1010BINDING SITE FOR RESIDUE CO A 766
5AC5SOFTWAREILE A:44 , CYS A:47 , LYS A:48 , CYS A:54 , HOH A:822BINDING SITE FOR RESIDUE CO A 767

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:113 -Pro A:114
2Leu A:207 -Pro A:208
3Asn A:210 -Pro A:211

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YWR)

(-) 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:216
 aligned with O67023_AQUAE | O67023 from UniProtKB/TrEMBL  Length:216

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
         O67023_AQUAE     1 MLKIGVLVSGRGSNLQAIIDAIESGKVNASIELVISDNPKAYAIERCKKHNVECKVIQRKEFPSKKEFEERMALELKKKGVELVVLAGFMRILSHNFLKYFPNKVINIHPSLIPAFQGLHAQKQAVEFGVKFSGCTVHIVDESVDAGPVIVQAVVPVLPEDDENTLADRILKWEHKILPQTVQWFAQDRIIIDGRKVIVKDATYGTLPVNPALEIF 216
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -2ywrA00 A:2-216  [code=3.40.50.170, no name defined]                                                                                                                                                                    CATH domains
               Pfam domains -Formyl_trans_N-2ywrA01 A:2-182                                                                                                                                                       ---------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhh....eeeeeeee....hhhhhhhhhhh..eee.hhhhh.hhhhhhhhhhhhhhhh...eeee.......hhhhhh.....eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeee.........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ywr A   1 mLKIGVLVSGRGSNLQAIIDAIESGKVNASIELVISDNPKAYAIERCKKHNVECKVIQRKEFPSKKEFEERmALELKKKGVELVVLAGFmRILSHNFLKYFPNKVINIHPSLIPAFQGLHAQKQAVEFGVKFSGCTVHIVDESVDAGPVIVQAVVPVLPEDDENTLADRILKWEHKILPQTVQWFAQDRIIIDGRKVIVKDATYGTLPVNPALEIF 216
                            |       10        20        30        40        50        60        70 |      80        90       100       110       120       130       140       150       160       170       180       190       200       210      
                            |                                                                     72-MSE            90-MSE                                                                                                                          
                            1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2YWR)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Formyl_trans_N] (25)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (O67023_AQUAE | O67023)
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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  2ywr
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