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(-) Description

Title :  PYLD HOLOENZYME
 
Authors :  F. Quitterer, P. Beck, A. Bacher, M. Groll
Date :  06 Feb 13  (Deposition) - 12 Jun 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Pyrrolysine, 22Nd Amino Acid, Biosynthesis, Rossmann Fold, Dehydrogenase, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Quitterer, P. Beck, A. Bacher, M. Groll
Structure And Reaction Mechanism Of Pyrrolysine Synthase (Pyld).
Angew. Chem. Int. Ed. Engl. V. 52 7033 2013
PubMed-ID: 23720358  |  Reference-DOI: 10.1002/ANIE.201301164

(-) Compounds

Molecule 1 - PYLD
    Chains: A, B
    EC Number: 1.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET28B
    Gene: MBAR_A0835
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 269797
    Strain: FUSARO

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NA2Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NA-1Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:121 , THR A:125 , VAL A:147 , GLY A:150 , LYS A:151 , VAL A:152 , TYR A:170 , ASP A:171 , ALA A:172 , LEU A:176 , ALA A:203 , THR A:204 , PRO A:205 , CYS A:206 , THR A:209 , PRO A:224 , ILE A:226 , GLU A:245 , PRO A:246 , LEU A:247 , MG A:903 , HOH A:1001 , HOH A:1015 , HOH A:1035 , HOH A:1066 , HOH A:1070 , HOH A:1075 , HOH A:1081BINDING SITE FOR RESIDUE NAD A 901
2AC2SOFTWAREGLU A:202 , THR A:204 , CYS A:206 , PRO A:227 , HOH A:1002BINDING SITE FOR RESIDUE NA A 902
3AC3SOFTWARETYR A:129 , GLU A:245 , LEU A:247 , ILE A:249 , GLY A:250 , NAD A:901BINDING SITE FOR RESIDUE MG A 903
4AC4SOFTWAREASN B:121 , THR B:125 , VAL B:147 , GLY B:150 , LYS B:151 , VAL B:152 , TYR B:170 , ASP B:171 , ALA B:172 , ASP B:173 , LEU B:176 , ALA B:203 , THR B:204 , PRO B:205 , CYS B:206 , THR B:209 , PRO B:224 , ILE B:226 , GLU B:245 , PRO B:246 , LEU B:247 , MG B:903 , HOH B:1009 , HOH B:1014 , HOH B:1017 , HOH B:1030 , HOH B:1031 , HOH B:1063 , HOH B:1065 , HOH B:1069 , HOH B:1075BINDING SITE FOR RESIDUE NAD B 901
5AC5SOFTWAREGLU B:202 , THR B:204 , CYS B:206 , PRO B:227BINDING SITE FOR RESIDUE NA B 902
6AC6SOFTWARETYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAD B:901BINDING SITE FOR RESIDUE MG B 903

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:206 -A:206

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:226 -Pro A:227
2Ile B:226 -Pro B:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J43)

(-) Exons   (0, 0)

(no "Exon" information available for 4J43)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee......hhhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j43 A   5 TPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    14        24        34        44        54||      68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258 
                                                                             55|                                                                                                                                                                                                       
                                                                              60                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhh..ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j43 B   4 LTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    13        23        33        43        53  ||    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
                                                                               56|                                                                                                                                                                                                       
                                                                                60
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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  (0, 0)

(no "SCOP Domain" information available for 4J43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J43)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  4j43
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  1.4.1.-
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 Related Entries

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        Q46E80_METBF | Q46E80: 4j49 4j4b 4j4h 4jk3 4q39 4q3a 4q3b 4q3c 4q3d 4q3e

(-) Related Entries Specified in the PDB File

3t7v PYLB IN COMPLEX WITH 3R-METHYL-D-ORNITHINE
4ffp PYLC IN COMPLEX WITH L-LYSINE-NE-D-ORNITHINE
4j49
4j4b
4j4h