Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA PROTEIN HEMK, AN N5-GLUTAMINE METHYLTRANSFERASE
 
Authors :  R. Agarwal, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Feb 04  (Deposition) - 17 Aug 04  (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 :  Structural Genomics, Protein Structure Initiative, Hemk Protein, Hypothetical Protein, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. K. Burley, S. Swaminathan
A Novel Mode Of Dimerization Via Formation Of A Glutamate Anhydride Crosslink In A Protein Crystal Structure.
Proteins V. 71 1038 2008
PubMed-ID: 18247349  |  Reference-DOI: 10.1002/PROT.21962
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEMK PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GLN3Mod. Amino AcidGLUTAMINE
2SAM3Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GLN2Mod. Amino AcidGLUTAMINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GLN2Mod. Amino AcidGLUTAMINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:100 , PRO A:102 , THR A:106 , ILE A:128 , GLY A:129 , THR A:130 , ILE A:135 , ASP A:151 , VAL A:152 , GLU A:179 , PHE A:180 , ASN A:197 , GLU A:217 , ALA A:218 , GLN A:400 , HOH A:401 , HOH A:404 , HOH A:405 , HOH A:415 , HOH A:421 , HOH A:444BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWAREPHE B:100 , PRO B:102 , THR B:106 , GLY B:129 , THR B:130 , ILE B:135 , ASP B:151 , VAL B:152 , GLU B:179 , PHE B:180 , ASN B:197 , GLU B:217 , ALA B:218 , GLN B:401 , HOH B:405 , HOH B:406 , HOH B:408 , HOH B:420 , HOH B:468BINDING SITE FOR RESIDUE SAM B 302
3AC3SOFTWAREPHE C:100 , PRO C:102 , GLY C:129 , THR C:130 , GLY C:131 , ALA C:134 , ASP C:151 , GLU C:179 , PHE C:180 , ASN C:197 , GLU C:217 , ALA C:218 , GLN C:402 , HOH C:405 , HOH C:407 , HOH C:408 , HOH C:410 , HOH C:413 , HOH C:414BINDING SITE FOR RESIDUE SAM C 303
4AC4SOFTWAREPHE A:100 , ARG A:103 , ASN A:197 , PRO A:198 , TYR A:200 , SAM A:301 , HOH A:496BINDING SITE FOR RESIDUE GLN A 400
5AC5SOFTWAREPHE B:100 , ARG B:103 , ASN B:197 , PRO B:198 , TYR B:200 , GLU B:246 , SAM B:302 , HOH B:416 , HOH B:477 , HOH B:478BINDING SITE FOR RESIDUE GLN B 401
6AC6SOFTWAREPHE C:100 , ARG C:103 , ASN C:197 , PRO C:198 , TYR C:200 , SAM C:303 , HOH C:416BINDING SITE FOR RESIDUE GLN C 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SG9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SG9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SG9)

(-) Exons   (0, 0)

(no "Exon" information available for 1SG9)

(-) 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:275
 aligned with PRMC_THEMA | Q9WYV8 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:275
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277     
           PRMC_THEMA     8 SGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
               SCOP domains d1sg9a_ A: N5-glutamine methyltransferase, HemK                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----1sg9A01 A:12-85 DNA helicase RuvA subunit, C-terminal domain              1sg9A02 A:86-281 Vaccinia Virus protein VP39                                                                                                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhheeee..eeee........hhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh.eeee.............hhhhhhhhhh......hhhhhhhhhhh.....eeeee....hhhhhhh.....eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sg9 A   8 SGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSQ 400
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   ||
                                                                                                                                                                                                                                                                                                           281|
                                                                                                                                                                                                                                                                                                            400


Chain B from PDB  Type:PROTEIN  Length:275
 aligned with PRMC_THEMA | Q9WYV8 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:275
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277     
           PRMC_THEMA     8 SGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
               SCOP domains d1sg9b_ B: N5-glutamine methyltransferase, HemK                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----1sg9B01 B:12-85 DNA helicase RuvA subunit, C-terminal domain              1sg9B02 B:86-281 Vaccinia Virus protein VP39                                                                                                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhh...hhhhhhheeee..eeee.........hhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhh..eeee.............hhhhhhhhhhh.....hhhhhhhhh.......eeeee....hhhhhhh.....eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sg9 B   8 SGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSQ 401
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   ||
                                                                                                                                                                                                                                                                                                           281|
                                                                                                                                                                                                                                                                                                            401


Chain C from PDB  Type:PROTEIN  Length:275
 aligned with PRMC_THEMA | Q9WYV8 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:275
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277     
           PRMC_THEMA     8 SGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
               SCOP domains d1sg9c_ C: N5-glutamine methyltransferase, HemK                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----1sg9C01 C:12-85 DNA helicase RuvA subunit, C-terminal domain              1sg9C02 C:86-281 Vaccinia Virus protein VP39                                                                                                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhheeee..eeee.........hhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhhhhh....eeee.............hhhhhhhhhh......hhhhhhhhh.......eeeee....hhhhhhh.....eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sg9 C   8 SGAERKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSQ 402
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277   ||
                                                                                                                                                                                                                                                                                                           281|
                                                                                                                                                                                                                                                                                                            402
   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  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SG9)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PRMC_THEMA | Q9WYV8)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    GO:0036009    protein-glutamine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamine = S-adenosyl-L-homocysteine + protein N-methyl-L-glutamine.
    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.
    GO:0018364    peptidyl-glutamine methylation    The addition of a methyl group to a glutamine residue in a protein.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GLN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sg9)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1sg9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PRMC_THEMA | Q9WYV8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PRMC_THEMA | Q9WYV8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRMC_THEMA | Q9WYV8: 1nv8 1nv9 1vq1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SG9)