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(-) Description

Title :  CRYSTAL STRUCTURE OF SAM-DEPENDENT O-METHYLTRANSFERASE FROM PATHOGENIC BACTERIUM LEPTOSPIRA INTERROGANS
 
Authors :  X. Hou, Z. Wei, W. Gong
Date :  13 Jul 06  (Deposition) - 04 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Modified Rossman Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Hou, Y. Wang, Z. Zhou, S. Bao, Y. Lin, W. Gong
Crystal Structure Of Sam-Dependent O-Methyltransferase From Pathogenic Bacterium Leptospira Interrogans.
J. Struct. Biol. V. 159 523 2007
PubMed-ID: 17561415  |  Reference-DOI: 10.1016/J.JSB.2007.04.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SAM-DEPENDENT O-METHYLTRANSFERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LEPTOSPIRA INTERROGANS
    Organism Taxid: 173

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
2SAH3Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:229 , ARG A:231 , LEU A:232 , HIS A:234 , HOH A:3133 , LYS C:57BINDING SITE FOR RESIDUE SO4 A1001
02AC2SOFTWARELYS B:57 , ARG B:229 , ARG B:231 , LEU B:232BINDING SITE FOR RESIDUE SO4 B1002
03AC3SOFTWARELYS A:57 , ARG C:229 , ARG C:231 , LEU C:232BINDING SITE FOR RESIDUE SO4 C1003
04AC4SOFTWAREARG A:22 , TYR C:209 , ASN C:210 , HOH C:3124BINDING SITE FOR RESIDUE SO4 C1004
05AC5SOFTWAREMET A:42 , GLN A:43 , GLY A:68 , THR A:69 , PHE A:70 , SER A:74 , ASP A:92 , VAL A:93 , ALA A:121 , ASP A:154 , ASP A:156 , TYR A:163 , HOH A:3106 , HOH A:3116BINDING SITE FOR RESIDUE SAH A2001
06AC6SOFTWAREMET B:42 , GLN B:43 , GLY B:68 , THR B:69 , PHE B:70 , SER B:74 , CYS B:91 , ASP B:92 , VAL B:93 , ALA B:121 , PHE B:152 , ASP B:154 , ASP B:156 , TYR B:163 , HOH B:3041BINDING SITE FOR RESIDUE SAH B2002
07AC7SOFTWAREMET C:42 , GLN C:43 , GLY C:68 , THR C:69 , PHE C:70 , SER C:74 , ASP C:92 , VAL C:93 , TRP C:97 , ALA C:121 , ASP C:154 , ASP C:156 , TYR C:163 , HOH C:3017 , HOH C:3114BINDING SITE FOR RESIDUE SAH C2003
08AC8SOFTWAREGLY A:60 , ASP A:149 , LYS A:172 , PEG A:3003 , HOH A:3148BINDING SITE FOR RESIDUE PEG A3001
09AC9SOFTWAREPEG A:3003 , GLY C:60 , LYS C:172BINDING SITE FOR RESIDUE PEG C3002
10BC1SOFTWAREILE A:58 , SER A:59 , PEG A:3001 , ILE C:58 , SER C:59 , GLY C:60 , PEG C:3002BINDING SITE FOR RESIDUE PEG A3003
11BC2SOFTWARETRP A:184 , ASP A:185BINDING SITE FOR RESIDUE PEG A3004
12BC3SOFTWARETRP C:184 , GLU C:195BINDING SITE FOR RESIDUE PEG C3005
13BC4SOFTWARELEU B:122 , ASN B:162 , HOH B:3093BINDING SITE FOR RESIDUE PEG B3006
14BC5SOFTWARELYS A:106 , GLU A:107 , HOH A:3165BINDING SITE FOR RESIDUE PEG A3007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HNK)

(-) 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:229
 aligned with Q8F8Y3_LEPIN | Q8F8Y3 from UniProtKB/TrEMBL  Length:231

    Alignment length:232
                                                                                                                                                                                                                                                              231   
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        |-  
         Q8F8Y3_LEPIN     3 RKNISLTESLEEYIFRNSVREPDSFLKLRKETGTLAQANMQISPEEGQFLNILTKISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALETLQVLIDSKSAPSWASDFAFGPSSIDLFFLDADKENYPNYYPLILKLLKPGGLLIADNVLWDGSVADLSHQEPSTVGIRKFNELVYNDSLVDVSLVPIADGVSLVRKR---   -
               SCOP domains d2hnka_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....hhhhhhhhhhhhh.---....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...hhhhh........eeeeee..hhhhhhhhhhhhhhheeeeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hnk A   3 RKNISLTESLEEYIFRNSVREPDSFLKLRKETGTL---NMQISPEEGQFLNILTKISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALETLQVLIDSKSAPSWASDFAFGPSSIDLFFLDADKENYPNYYPLILKLLKPGGLLIADNVLWDGSVADLSHQEPSTVGIRKFNELVYNDSLVDVSLVPIADGVSLVRKRLEH 234
                                    12        22        32    |   42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
                                                             37  41                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with Q8F8Y3_LEPIN | Q8F8Y3 from UniProtKB/TrEMBL  Length:231

    Alignment length:233
                                                                                                                                                                                                                                                               231   
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
         Q8F8Y3_LEPIN     2 SRKNISLTESLEEYIFRNSVREPDSFLKLRKETGTLAQANMQISPEEGQFLNILTKISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALETLQVLIDSKSAPSWASDFAFGPSSIDLFFLDADKENYPNYYPLILKLLKPGGLLIADNVLWDGSVADLSHQEPSTVGIRKFNELVYNDSLVDVSLVPIADGVSLVRKR---   -
               SCOP domains d2hnkb_ B: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh....hhhhhhhhhhhhh...-....hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh...hhhhh........eeeeee..hhhhhhhhhhhhhhheeeeeeeeee..hhhhh.......hhhhhhhhhhhhhhhhh..eeeeee.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hnk B   2 SRKNISLTESLEEYIFRNSVREPDSFLKLRKETGTLAQ-NMQISPEEGQFLNILTKISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALETLQVLIDSKSAPSWASDFAFGPSSIDLFFLDADKENYPNYYPLILKLLKPGGLLIADNVLWDGSVADLSHQEPSTVGIRKFNELVYNDSLVDVSLVPIADGVSLVRKRLEH 234
                                    11        21        31       |41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
                                                                39 |                                                                                                                                                                                                 
                                                                  41                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:231
 aligned with Q8F8Y3_LEPIN | Q8F8Y3 from UniProtKB/TrEMBL  Length:231

    Alignment length:231
                                                                                                                                                                                                                                                              231  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        |- 
         Q8F8Y3_LEPIN     3 RKNISLTESLEEYIFRNSVREPDSFLKLRKETGTLAQANMQISPEEGQFLNILTKISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALETLQVLIDSKSAPSWASDFAFGPSSIDLFFLDADKENYPNYYPLILKLLKPGGLLIADNVLWDGSVADLSHQEPSTVGIRKFNELVYNDSLVDVSLVPIADGVSLVRKR--   -
               SCOP domains d2hnkc_ C: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhhh................eeeeee..hhhhhhhhhhhhhhheeeeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hnk C   3 RKNISLTESLEEYIFRNSVREPDSFLKLRKETGTLAQANMQISPEEGQFLNILTKISGAKRIIEIGTFTGYSSLCFASALPEDGKILCCDVSEEWTNVARKYWKENGLENKIFLKLGSALETLQVLIDSKSAPSWASDFAFGPSSIDLFFLDADKENYPNYYPLILKLLKPGGLLIADNVLWDGSVADLSHQEPSTVGIRKFNELVYNDSLVDVSLVPIADGVSLVRKRLE 233
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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  (1, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8F8Y3_LEPIN | Q8F8Y3)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

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