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(-) Description

Title :  PYLD IN COMPLEX WITH PYRROLYSINE AND NADH
 
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  (2x)
Biol. Unit 4:  B  (2x)
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 (2x): A 
Biological Unit 4 (2x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (7, 13)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4NA2Ligand/IonSODIUM ION
5NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7PYL2Ligand/IonPYRROLYSINE
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
7PYL1Ligand/IonPYRROLYSINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
6PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
7PYL1Ligand/IonPYRROLYSINE
Biological Unit 3 (5, 12)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL4Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
7PYL2Ligand/IonPYRROLYSINE
Biological Unit 4 (3, 6)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4NA-1Ligand/IonSODIUM ION
5NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
6PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
7PYL2Ligand/IonPYRROLYSINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:2 , ASN 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 , PYL A:904 , HOH A:1001 , HOH A:1006 , HOH A:1009 , HOH A:1111 , HOH A:1121BINDING SITE FOR RESIDUE NAI 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 , NAI A:901BINDING SITE FOR RESIDUE MG A 903
04AC4SOFTWAREALA A:2 , LEU A:3 , LEU A:4 , PRO A:52 , VAL A:53 , GLY A:58 , ILE A:59 , ILE A:60 , PHE A:63 , ALA A:103 , ASP A:104 , PHE A:108 , NAI A:901 , HOH A:1003 , HOH A:1004 , HOH A:1019 , HOH A:1030 , HOH A:1116BINDING SITE FOR RESIDUE PYL A 904
05AC5SOFTWARELYS A:18 , ALA A:19 , LEU A:242 , ALA A:244 , HOH A:1055BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWARELYS A:32 , GLN A:72 , TYR A:73 , ASP A:77 , SER A:78 , HOH A:1012 , HOH A:1077 , HOH A:1126BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWAREPHE A:79 , GLU A:91 , HOH A:1138BINDING SITE FOR RESIDUE EDO A 907
08AC8SOFTWAREMET A:1 , ALA A:2 , PRO A:205 , CYS A:206 , MET B:1 , PRO B:205 , CYS B:206BINDING SITE FOR RESIDUE PEG A 908
09AC9SOFTWAREHOH A:1086 , ALA B:2 , ASN B:121 , THR B:125 , GLY B:150 , LYS B:151 , VAL B:152 , TYR B:170 , ASP B:171 , ALA B:172 , ALA B:203 , THR B:204 , PRO B:205 , THR B:209 , PRO B:224 , ILE B:226 , GLU B:245 , PRO B:246 , LEU B:247 , MG B:903 , PYL B:904 , HOH B:1002 , HOH B:1003 , HOH B:1013 , HOH B:1016 , HOH B:1018BINDING SITE FOR RESIDUE NAI B 901
10BC1SOFTWAREGLU B:202 , THR B:204 , CYS B:206 , PRO B:227 , ALA B:229 , HOH B:1001BINDING SITE FOR RESIDUE NA B 902
11BC2SOFTWARETYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAI B:901BINDING SITE FOR RESIDUE MG B 903
12BC3SOFTWARELEU B:3 , LEU B:4 , PRO B:52 , VAL B:53 , GLY B:58 , ILE B:59 , ILE B:60 , ALA B:103 , PHE B:108 , NAI B:901 , HOH B:1004 , HOH B:1005 , HOH B:1031 , HOH B:1032BINDING SITE FOR RESIDUE PYL B 904
13BC4SOFTWARELEU B:242 , ILE B:243 , ALA B:244BINDING SITE FOR RESIDUE EDO B 905

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A: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 4Q39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q39)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q39)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               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..hhhhhhhhhhhhh.ee..........eeee........hhhhh....eee........hhhhhhhh..eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q39 A   1 MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               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..hhhhhhhhhhhhh.ee........eeeeee........hhh.eeeeeeee........hhhhhhhh..eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q39 B   1 MALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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 4Q39)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q39)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  1.4.1.-
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q46E80_METBF | Q46E80: 4j43 4j49 4j4b 4j4h 4jk3 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
4j4h PYLD IN COMPLEX WITH PYRROLINE-CARBOXY-LYSINE
4q3a
4q3b
4q3c
4q3d
4q3e