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(-) Description

Title :  PYLC IN COMPLEX WITH L-LYSINE-NE-D-ORNITHINE (COCRYSTALLIZED WITH L-LYSINE AND D-ORNITHINE)
 
Authors :  F. Quitterer, A. List, P. Beck, A. Bacher, M. Groll
Date :  01 Jun 12  (Deposition) - 19 Sep 12  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Amino Acid, Biosynthesis Of Pyrrolysine, Isopeptide Bond Formation, Atp-Grasp Fold, Ligase, Atp-Binding, L-Lysine And 3R-Methyl-D- Ornithine, Cytosol, Ligase-Product Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Quitterer, A. List, P. Beck, A. Bacher, M. Groll
Biosynthesis Of The 22Nd Genetically Encoded Amino Acid Pyrrolysine: Structure And Reaction Mechanism Of Pylc At 1. 5A Resolution.
J. Mol. Biol. V. 424 270 2012
PubMed-ID: 22985965  |  Reference-DOI: 10.1016/J.JMB.2012.09.007

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PET28B
    Gene: MBAR_A0837
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 269797
    Strain: FUSARO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
10TF1Ligand/IonN~6~-D-ORNITHYL-L-LYSINE
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:10 , LEU A:11 , GLN A:12 , GLU A:72 , SER A:137 , SER A:169 , GLU A:171 , ASP A:225 , ARG A:243 , PRO A:245 , SER A:246 , GLN A:247 , THR A:248 , GLU A:302 , PO4 A:903 , ADP A:906 , HOH A:1001 , HOH A:1149BINDING SITE FOR RESIDUE 0TF A 901
2AC2SOFTWARELYS A:104 , PHE A:129 , LYS A:131 , GLU A:135 , SER A:136 , SER A:137 , SER A:138 , GLU A:160 , GLU A:161 , TYR A:162 , VAL A:163 , ILE A:189 , GLU A:227 , ILE A:229 , GLU A:239 , PO4 A:903 , MG A:904 , MG A:905 , HOH A:1011 , HOH A:1017 , HOH A:1168 , HOH A:1203BINDING SITE FOR RESIDUE ADP A 902
3AC3SOFTWARESER A:136 , SER A:137 , GLU A:227 , GLU A:239 , ASP A:241 , ARG A:243 , 0TF A:901 , ADP A:902 , MG A:904 , MG A:905 , HOH A:1017BINDING SITE FOR RESIDUE PO4 A 903
4AC4SOFTWAREGLU A:227 , GLU A:239 , ADP A:902 , PO4 A:903 , MG A:905 , HOH A:1168BINDING SITE FOR RESIDUE MG A 904
5AC5SOFTWARELYS A:104 , GLU A:239 , ASP A:241 , ADP A:902 , PO4 A:903 , MG A:904 , HOH A:1203BINDING SITE FOR RESIDUE MG A 905
6AC6SOFTWAREGLY A:8 , LYS A:10 , ASP A:31 , LYS A:32 , PHE A:48 , ASP A:49 , VAL A:50 , ILE A:51 , ASN A:71 , GLU A:72 , ASN A:73 , 0TF A:901 , HOH A:1033 , HOH A:1092 , HOH A:1149BINDING SITE FOR RESIDUE ADP A 906

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FFP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:126 -Pro A:127
2Leu A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FFP)

(-) Sequences/Alignments

Asymmetric/Biological 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    
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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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeeee............eeee.....hhhhhhhhhh...eeee...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.............eeee..........eee.......eeee....eeeeeeeeee...eee...eeeee.....eeeeee...hhhhhhhhhhhhhh...eeeeeeeeeee..eeeeeeee.....hhhhhhhhhhh.hhhhhhhhhh..........eeeeeeeee.hhh.eee.hhhhhh...eeeeeeee..eeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ffp A   1 MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDVIKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRISRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPDTLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPLFRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSSGINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSDYGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFGAVL 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140    || 156       166       176       186       196       206       216       226       236       246       256       266       280       290       300       310       320       330       340       350       360   
                                                                                                                                                                          145|                                                                                                                        275|                                                                                   
                                                                                                                                                                           152                                                                                                                         280
   Legend:   → Mismatch (orange background)
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  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 4FFP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q46E79_METBF | Q46E79: 4ffl 4ffm 4ffn 4ffo 4ffr

(-) Related Entries Specified in the PDB File

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