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(-) Description

Title :  PYLD COCRYSTALLIZED WITH L-LYSINE-NE-L-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 :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),B (1x)
Biol. Unit 6:  C (1x),D (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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x)B (1x)  
Biological Unit 6 (1x):   C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 24)

Asymmetric Unit (7, 24)
No.NameCountTypeFull Name
12YG4Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL4Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5NA4Ligand/IonSODIUM ION
6NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
12YG1Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
12YG1Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
12YG1Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
12YG1Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 5 (4, 8)
No.NameCountTypeFull Name
12YG1Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 6 (2, 2)
No.NameCountTypeFull Name
12YG1Ligand/IonN~6~-L-LYSYL-L-LYSINE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5NA-1Ligand/IonSODIUM ION
6NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
7PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:121 , THR A:125 , GLY A:150 , LYS A:151 , VAL A:152 , ASP A:171 , ALA A:172 , ASP A:173 , ALA A:203 , THR A:204 , PRO A:205 , THR A:209 , PRO A:224 , ILE A:226 , GLU A:245 , PRO A:246 , LEU A:247 , MG A:903 , 2YG A:904 , HOH A:1005 , HOH A:1014 , HOH A:1048 , HOH A:1049 , HOH A:1088BINDING 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
04AC4SOFTWARELEU A:4 , VAL A:53 , GLY A:58 , ILE A:59 , ILE A:60 , PHE A:63 , ALA A:103 , ASP A:104 , ASN A:121 , PRO A:246 , NAD A:901 , HOH A:1011 , HOH A:1057 , HOH A:1060 , HOH A:1071BINDING SITE FOR RESIDUE 2YG A 904
05AC5SOFTWARELYS A:18 , ALA A:19 , LEU A:242 , ALA A:244BINDING SITE FOR RESIDUE GOL A 905
06AC6SOFTWARELEU A:38 , TYR A:39 , HOH A:1039 , HOH A:1084 , ARG B:135BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWAREVAL A:161 , PHE A:165 , VAL A:167 , GLY A:185 , HOH A:1033 , HOH B:1095BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWARELEU A:9 , ASN A:11 , ILE A:12 , ALA A:65 , SER A:66 , HOH A:1113BINDING SITE FOR RESIDUE EDO A 908
09AC9SOFTWAREGLU A:131 , SER A:134 , LYS A:163 , PHE A:165 , HOH A:1098 , HOH A:1106 , HOH A:1123BINDING SITE FOR RESIDUE EDO A 909
10BC1SOFTWARETHR A:27 , ARG A:135 , LEU A:137BINDING SITE FOR RESIDUE EDO A 910
11BC2SOFTWAREALA B:2 , ASN 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 , 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 , 2YG B:904 , HOH B:1017 , HOH B:1018 , HOH B:1037 , HOH B:1103 , HOH B:1111BINDING SITE FOR RESIDUE NAD B 901
12BC3SOFTWAREGLU B:202 , THR B:204 , CYS B:206 , PRO B:227 , HOH B:1091BINDING SITE FOR RESIDUE NA B 902
13BC4SOFTWARETYR B:129 , GLU B:245 , LEU B:247 , ILE B:249 , GLY B:250 , NAD B:901BINDING SITE FOR RESIDUE MG B 903
14BC5SOFTWARELEU B:3 , LEU B:4 , VAL B:53 , GLY B:58 , ILE B:59 , ILE B:60 , PHE B:63 , ALA B:103 , ASP B:104 , ASN B:121 , PRO B:246 , LEU B:247 , NAD B:901 , HOH B:1003 , HOH B:1023 , HOH B:1080 , HOH B:1108BINDING SITE FOR RESIDUE 2YG B 904
15BC6SOFTWARELYS A:32 , TYR A:73 , HOH A:1003 , GLN B:72 , ASP B:77 , SER B:78BINDING SITE FOR RESIDUE GOL B 905
16BC7SOFTWARESER A:55 , ASP A:85 , ASP B:85 , MET B:102BINDING SITE FOR RESIDUE PEG B 906
17BC8SOFTWAREALA C:2 , ASN C:121 , GLY C:150 , LYS C:151 , VAL C:152 , ASP C:171 , ALA C:172 , ASP C:173 , LEU C:176 , THR C:204 , PRO C:205 , THR C:209 , PRO C:224 , ILE C:226 , GLU C:245 , PRO C:246 , LEU C:247 , MG C:903 , HOH C:1003 , HOH C:1010 , HOH C:1013BINDING SITE FOR RESIDUE NAD C 901
18BC9SOFTWAREGLU C:202 , THR C:204 , CYS C:206 , GLY C:225 , PRO C:227BINDING SITE FOR RESIDUE NA C 902
19CC1SOFTWARETYR C:129 , GLU C:245 , LEU C:247 , ILE C:249 , GLY C:250 , NAD C:901BINDING SITE FOR RESIDUE MG C 903
20CC2SOFTWARELEU C:3 , LEU C:4 , PRO C:52 , VAL C:53 , GLY C:58 , ILE C:59 , ILE C:60 , PHE C:63 , ALA C:103 , HOH C:1004 , HOH C:1006 , HOH C:1014BINDING SITE FOR RESIDUE 2YG C 904
21CC3SOFTWAREHOH A:1091 , ASN D:121 , VAL D:147 , GLY D:150 , LYS D:151 , VAL D:152 , TYR D:170 , ASP D:171 , ALA D:172 , ALA D:203 , THR D:204 , PRO D:205 , THR D:209 , PRO D:224 , ILE D:226 , GLU D:245 , PRO D:246 , MG D:903 , 2YG D:904 , HOH D:1002 , HOH D:1003 , HOH D:1005 , HOH D:1011BINDING SITE FOR RESIDUE NAD D 901
22CC4SOFTWAREGLU D:202 , THR D:204 , CYS D:206 , PRO D:227BINDING SITE FOR RESIDUE NA D 902
23CC5SOFTWARETYR D:129 , GLU D:245 , PRO D:246 , LEU D:247 , GLY D:248 , ILE D:249 , GLY D:250 , NAD D:901BINDING SITE FOR RESIDUE MG D 903
24CC6SOFTWARELEU D:3 , LEU D:4 , PRO D:52 , VAL D:53 , GLY D:58 , ILE D:59 , ILE D:60 , PHE D:63 , ALA D:103 , NAD D:901 , HOH D:1001 , HOH D:1004 , HOH D:1010BINDING SITE FOR RESIDUE 2YG D 904

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:206 -D:206
2B:206 -C:206

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ile A:226 -Pro A:227
2Ile B:226 -Pro B:227
3Ile C:226 -Pro C:227
4Ile D:226 -Pro D:227

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q3C)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q3C)

(-) 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......eeeee..........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
                 4q3c 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...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3c 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         


Chain C 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...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4q3c C   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 D from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               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........hhhhhhhhh.eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4q3c D   2 ALLTPDDLININMQLQKADSAVQEVTGLDIKGICKALYGTFSSSEKVGIVPVTSGNGIIGNFSASLHAITQYFGFDSFVTDMPDVSGYYEAVQNGAEIILMADDRTFLAHNLKNGKMANNQPCTGIIYAEIASRYLKADSKDVLVVGLGKVGFPGAEHLVQKDFRVYGYDADETLLERATSNLGIIPFDPANPKKFSIIFEATPCANTIPEAVLSENCVLSTPGIPCAISEELRDKYEVQLIAEPLGIGTASMLYSVL 259
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 4Q3C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q3C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q3C)

(-) Gene Ontology  (2, 2)

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  4q3c
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  1.4.1.-
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  (no 'MIM ID' available)
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    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
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  Q46E80_METBF | Q46E80
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 Related Entries

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

UniProtKB/TrEMBL
        Q46E80_METBF | Q46E80: 4j43 4j49 4j4b 4j4h 4jk3 4q39 4q3a 4q3b 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
4q39 PYLD IN COMPLEX WITH PYRROLYSINE
4q3a
4q3b
4q3d
4q3e