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(-) Description

Title :  PYLD COCRYSTALLIZED WITH L-ORNITHINE-ND-D-LYSINE AND NAD+
 
Authors :  F. Quitterer, P. Beck, A. Bacher, M. Groll
Date :  11 Apr 14  (Deposition) - 23 Apr 14  (Release) - 20 Aug 14  (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 (1x),B (1x)
Keywords :  Rossmann Fold, Dehydrogenase, Pyrrolysine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Quitterer, P. Beck, A. Bacher, M. Groll
The Formation Of Pyrroline And Tetrahydropyridine Rings In Amino Acids Catalyzed By Pyrrolysine Synthase (Pyld).
Angew. Chem. Int. Ed. Engl. V. 53 8150 2014
PubMed-ID: 24916332  |  Reference-DOI: 10.1002/ANIE.201402595

(-) Compounds

Molecule 1 - PYLD, PYRROLYSINE SYNTHASE
    Chains: A, B
    EC Number: 1.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 13)

Asymmetric Unit (7, 13)
No.NameCountTypeFull Name
12YJ2Ligand/IonN~5~-D-LYSYL-L-ORNITHINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5NA2Ligand/IonSODIUM ION
6NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
12YJ1Ligand/IonN~5~-D-LYSYL-L-ORNITHINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
12YJ1Ligand/IonN~5~-D-LYSYL-L-ORNITHINE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (4, 5)
No.NameCountTypeFull Name
12YJ1Ligand/IonN~5~-D-LYSYL-L-ORNITHINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7SO41Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN 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 , ASP A:173 , 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 , 2YJ A:904 , SO4 A:907 , HOH A:1001 , HOH A:1002 , HOH A:1011 , HOH A:1013 , HOH A:1018 , HOH A:1025 , HOH A:1029 , HOH A:1063 , HOH A:1091 , HOH A:1105BINDING SITE FOR RESIDUE NAD A 901
02AC2SOFTWAREGLU A:202 , THR A:204 , CYS A:206 , PRO A:227BINDING SITE FOR RESIDUE NA A 902
03AC3SOFTWARETYR A:129 , GLU A:245 , LEU A:247 , ILE A:249 , GLY A:250 , NAD A:901BINDING SITE FOR RESIDUE MG A 903
04AC4SOFTWAREVAL A:53 , ILE A:60 , PHE A:63 , ALA A:103 , ASP A:104 , ASP A:105 , ILE A:226 , NAD A:901 , SO4 A:907 , HOH A:1003 , HOH A:1022 , HOH A:1031 , HOH A:1032 , HOH A:1043BINDING SITE FOR RESIDUE 2YJ A 904
05AC5SOFTWARELEU A:242 , ALA A:244BINDING SITE FOR RESIDUE EDO A 905
06AC6SOFTWAREILE A:226 , PRO A:246BINDING SITE FOR RESIDUE EDO A 906
07AC7SOFTWARENAD A:901 , 2YJ A:904 , HOH A:1018 , HOH A:1088 , HOH A:1105BINDING SITE FOR RESIDUE SO4 A 907
08AC8SOFTWAREASN 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 , 2YJ B:904 , EDO B:906 , HOH B:1002 , HOH B:1003 , HOH B:1010 , HOH B:1033 , HOH B:1047 , HOH B:1051 , HOH B:1082BINDING SITE FOR RESIDUE NAD B 901
09AC9SOFTWAREGLU B:202 , THR B:204 , CYS B:206 , PRO B:227 , HOH B:1005BINDING SITE FOR RESIDUE NA B 902
10BC1SOFTWARETYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAD B:901BINDING SITE FOR RESIDUE MG B 903
11BC2SOFTWAREPRO B:52 , VAL B:53 , ILE B:60 , PHE B:63 , ALA B:103 , ASP B:104 , ASP B:105 , NAD B:901 , EDO B:906 , HOH B:1001 , HOH B:1012 , HOH B:1020 , HOH B:1036BINDING SITE FOR RESIDUE 2YJ B 904
12BC3SOFTWAREASP A:85 , MET A:102 , ASP B:85 , TYR B:89 , MET B:102BINDING SITE FOR RESIDUE GOL B 905
13BC4SOFTWARENAD B:901 , 2YJ B:904BINDING SITE FOR RESIDUE EDO B 906

(-) 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 4Q3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q3E)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q3E)

(-) 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: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........hhhhhhhhh.eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3e A   3 LLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    12        22        32        42        52  ||    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256   
                                                                               55|                                                                                                                                                                                                       
                                                                                60                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh......eeee...........hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh...eeeee....eeeee.....eeehhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3e B   5 TPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   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 4Q3E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q3E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q3E)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        Q46E80_METBF | Q46E80: 4j43 4j49 4j4b 4j4h 4jk3 4q39 4q3a 4q3b 4q3c 4q3d

(-) 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
4q39 PYLD IN COMPLEX WITH PYRROLYSINE
4q3a
4q3b
4q3c
4q3d