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(-) Description

Title :  PYLD HOLOENZYME SOAKED WITH L-LYSINE-NE-D-ORNITHINE
 
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, L-Lysine-Ne-3R-Methyl-D-Ornithine, 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  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
11J11Ligand/IonN~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2MG2Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION
4NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11J1-1Ligand/IonN~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION
4NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5NAI-1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
11J11Ligand/IonN~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION
4NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
11J12Ligand/IonN~6~-[(2R)-3,4-DIHYDRO-2H-PYRROL-2-YLCARBONYL]-L-LYSINE
2MG-1Ligand/IonMAGNESIUM ION
3NA-1Ligand/IonSODIUM ION
4NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:121 , THR A:125 , 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:1017 , HOH A:1021 , HOH A:1024 , HOH A:1039 , HOH A:1048 , HOH A:1080 , HOH A:1086 , HOH A:1087 , HOH A:1095BINDING 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 , LEU B:176 , 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:904 , HOH B:1001 , HOH B:1015 , HOH B:1030 , HOH B:1049 , HOH B:1050 , HOH B:1062BINDING SITE FOR RESIDUE NAI B 901
5AC5SOFTWARELEU B:4 , PRO B:52 , VAL B:53 , ILE B:59 , ILE B:60 , PHE B:63 , ALA B:103 , HOH B:1003 , HOH B:1033 , HOH B:1082BINDING SITE FOR RESIDUE 1J1 B 902
6AC6SOFTWAREGLU B:202 , THR B:204 , CYS B:206 , PRO B:227 , HOH B:1005BINDING SITE FOR RESIDUE NA B 903
7AC7SOFTWARETYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAI B:901BINDING SITE FOR RESIDUE MG B 904

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:206 -B: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 4J49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J49)

(-) Exons   (0, 0)

(no "Exon" information available for 4J49)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee......hhhhhhhhhhhh..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
                 4j49 A   4 LTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    13        23        33        43        53 ||     69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
                                                                              55|                                                                                                                                                                                                     
                                                                               62                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee...........hhhhhhhhhhhhh..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
                 4j49 B   3 LLTPDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                               ||   13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
                               6|                                                                                                                                                                                                                                                           
                                8
   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  (0, 0)

(no "SCOP Domain" information available for 4J49)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J49)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J49)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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        Q46E80_METBF | Q46E80: 4j43 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
4j43
4j4b
4j4h