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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLORNITHINE SYNTHASE (PYLB)
 
Authors :  F. Quitterer, A. List, W. Eisenreich, A. Bacher, M. Groll
Date :  31 Jul 11  (Deposition) - 30 Nov 11  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim-Barrel Fold, Mutase, [4Fe-4S]-Cluster, Sam, Lysine, 3- Methylornithine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Quitterer, A. List, W. Eisenreich, A. Bacher, M. Groll
Crystal Structure Of Methylornithine Synthase (Pylb): Insights Into The Pyrrolysine Biosynthesis.
Angew. Chem. Int. Ed. Engl. V. 51 1339 2012
PubMed-ID: 22095926  |  Reference-DOI: 10.1002/ANIE.201106765

(-) Compounds

Molecule 1 - METHYLORNITHINE SYNTHASE PYLB
    Chains: A
    EC Number: 2.8.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: SOLUBL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MBAR_A0838
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 269797
    Strain: FUSARO / DSM 804

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MD01Ligand/Ion5-AMINO-D-ISOLEUCINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:71 , ASN A:73 , CYS A:75 , CYS A:78 , ASN A:81 , ARG A:182 , SAM A:992BINDING SITE FOR RESIDUE SF4 A 991
2AC2SOFTWAREPHE A:77 , THR A:114 , MET A:115 , TYR A:169 , GLU A:171 , ARG A:182 , ARG A:190 , LEU A:209 , MET A:237 , THR A:238 , PHE A:239 , LEU A:240 , GLN A:242 , VAL A:310 , HOH A:354 , HOH A:359 , HOH A:363 , SF4 A:991 , MD0 A:993BINDING SITE FOR RESIDUE SAM A 992
3AC3SOFTWAREPHE A:64 , ASP A:112 , SER A:146 , TYR A:169 , ARG A:235 , SER A:277 , ASP A:279 , THR A:298 , SER A:299 , HOH A:357 , HOH A:362 , SAM A:992BINDING SITE FOR RESIDUE MD0 A 993

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T7V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T7V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T7V)

(-) Exons   (0, 0)

(no "Exon" information available for 3T7V)

(-) 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    
   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:337
 aligned with PYLB_METBF | Q46E78 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:337
                                    21        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       281       291       301       311       321       331       341       
           PYLB_METBF    12 SLGDKVIEGYQLTDNDLRTLLSLESKEGLERLYSAARKVRDHYFGNRVFLNCFIYFSTYCKNQCSFCYYNCRNEINRYRLTMEEIKETCKTLKGAGFHMVDLTMGEDPYYYEDPNRFVELVQIVKEELGLPIMISPGLMDNATLLKAREKGANFLALYQETYDTELYRKLRVGQSFDGRVNARRFAKQQGYCVEDGILTGVGNDIESTILSLRGMSTNDPDMVRVMTFLPQEGTPLEGFRDKSNLSELKIISVLRLMFPKRLIPASLDLEGIDGMVLRLNAGANIVTSILPPDSQLEGVANYDRDLEERDRDIKSVVRRLEIMGMKPARQADFEAVL 348
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.......................hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh.eeeee......hhhhhhhhh...hhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhh.....eeehhhhhhhhhhhhhhh...eeeee......................hhhhhhhhhhhhh.ee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t7v A  12 SLGDKVIEGYQLTDNDLRTLLSLESKEGLERLYSAARKVRDHYFGNRVFLNCFIYFSTYCKNQCSFCYYNCRNEINRYRLTMEEIKETCKTLKGAGFHMVDLTMGEDPYYYEDPNRFVELVQIVKEELGLPIMISPGLMDNATLLKAREKGANFLALYQETYDTELYRKLRVGQSFDGRVNARRFAKQQGYCVEDGILTGVGNDIESTILSLRGMSTNDPDMVRVMTFLPQEGTPLEGFRDKSNLSELKIISVLRLMFPKRLIPASLDLEGIDGMVLRLNAGANIVTSILPPDSQLEGVANYDRDLEERDRDIKSVVRRLEIMGMKPARQADFEAVL 348
                                    21        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       281       291       301       311       321       331       341
   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  (0, 0)

(no "SCOP Domain" information available for 3T7V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T7V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T7V)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PYLB_METBF | Q46E78)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0016866    intramolecular transferase activity    Catalysis of the transfer of a functional group from one position to another within a single molecule.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    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:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0071524    pyrrolysine biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrrolysine, N6-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine.

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  3t7v
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  PYLB_METBF | Q46E78
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 Related Entries

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(-) Related Entries Specified in the PDB File

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