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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE CLASS I S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE (LMO1582) FROM LISTERIA MONOCYTOGENES AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Dec 05  (Deposition) - 17 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of (16411011) From Listeria Monocytogenes Li2 At 2. 20 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN LMO1582
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: 16411011
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 1639
    Strain: LI2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL5Ligand/IonGLYCEROL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
5SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:171BINDING SITE FOR RESIDUE CL A 333
2AC2SOFTWARELYS A:117 , LYS A:118 , ASN A:119BINDING SITE FOR RESIDUE SO4 A 334
3AC3SOFTWAREASN A:94 , HIS A:95 , GLN A:96 , MSE A:97 , THR A:98 , PRO A:125 , ALA A:126 , CYS A:127 , GLY A:128 , THR A:129 , ASN A:131 , LEU A:132 , ASP A:154 , VAL A:155 , ASP A:156 , LEU A:159 , ASP A:180 , GLY A:181 , ASP A:196 , PRO A:198 , PHE A:226 , HOH A:414 , HOH A:452BINDING SITE FOR RESIDUE SAM A 400
4AC4SOFTWARETYR A:239 , GLU A:268 , LYS A:298 , PRO A:299 , PRO A:300 , TRP A:327 , PHE A:328 , GOL A:404 , HOH A:497BINDING SITE FOR RESIDUE GOL A 401
5AC5SOFTWARETYR A:201 , GLY A:218 , HIS A:219 , LYS A:262 , GLY A:265BINDING SITE FOR RESIDUE GOL A 402
6AC6SOFTWAREARG A:215 , GLU A:216 , GLU A:217BINDING SITE FOR RESIDUE GOL A 403
7AC7SOFTWAREPRO A:300 , LYS A:301 , GLU A:302 , TRP A:327 , GOL A:401BINDING SITE FOR RESIDUE GOL A 404
8AC8SOFTWARETHR A:276 , SER A:310 , LEU A:311 , THR A:312 , HOH A:495BINDING SITE FOR RESIDUE GOL A 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2F8L)

(-) 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    
   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:323
 aligned with Q8Y6U9_LISMO | Q8Y6U9 from UniProtKB/TrEMBL  Length:332

    Alignment length:328
                                    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       261       271       281       291       301       311       321        
         Q8Y6U9_LISMO     2 ANEATQELFQVLDNTAIILQNELEISYLEAVYETGENLFQKEVLQKEELSSEKQLKLQESYESIELENFSNEEIRKGLQLALLKGMKHGIQVNHQMTPDSIGFIVAYLLEKVIQKKKNISILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLALVGADLQRQKMTLLHQDGLANLLVDPVDVVISDLPVGYYPDDENAKTFELCREEGHSFAHFLFIEQGMRYTKPGGYLFFLVPDAMFGTSDFAKVDKFIKKNGHIEGIIKLPETLFKSEQARKSILILRKADVNVKPPKEVLLANLSSLTDPSVTAPILAEIENWFK 329
               SCOP domains d2f8la1 A:2-329 Hypothetical protein Lmo1582                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......----hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhhhh...eeee...........eeeeeee....ee.hhhhhh..........eehhhhhhhhhhhheeeeeeeeeeee.hhhhhhhhhhhhhhhhhheeeeeeee.hhhhh..-...eeeeeeee...........eeee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f8l A   2 ANEATQELFQVLDNTAIILQNELEISYLEAVYETGENLFQKEVLQKEE----KQLKLQASYESIELENFSNEEIRKGLQLALLKGmKHGIQVNHQmTPDSIGFIVAYLLEKVIQKKKNVSILDPACGTANLLTTVINQLELKGDVDVHASGVDVDDLLISLALVGADLQRQKmTLLHQDGLANLLVDPVDVVISDLPVGYYPDDENAKTFELCREEGHSFAHFLFIEQGmRYTKPGGYLFFLVPDAmFGTSDFAKVDKFIKKNGHIEGIIKLPETLFKS-QARKSILILEKADVDVKPPKEVLLANLSSLTDPSVTAPILAEIENWFK 329
                                    11        21        31        41       | -  |     61        71        81     |  91     | 101       111       121       131       141       151       161       171  |    181       191       201       211       221       231       241      |251       261       271        |-|      291       301       311       321        
                                                                          49   54                               87-MSE    97-MSE                                                                      174-MSE                                                  231-MSE          248-MSE                         280 |                                               
                                                                                                                                                                                                                                                                                                                  282
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F8L)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8Y6U9_LISMO | Q8Y6U9)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008170    N-methyltransferase activity    Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.

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