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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SULFITE MTMB COMPLEX
 
Authors :  B. Hao, G. Zhao, P. T. Kang, J. A. Soares, T. K. Ferguson, J. Gallucci, J. A M. K. Chan
Date :  26 Jun 04  (Deposition) - 19 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Hao, G. Zhao, P. T. Kang, J. A. Soares, T. K. Ferguson, J. Gallucci, J. A. Krzycki, M. K. Chan
Reactivity And Chemical Synthesis Of L-Pyrrolysine- The 22(Nd) Genetically Encoded Amino Acid
Chem. Biol. V. 11 1317 2004
PubMed-ID: 15380192  |  Reference-DOI: 10.1016/J.CHEMBIOL.2004.07.011

(-) Compounds

Molecule 1 - MONOMETHYLAMINE METHYLTRANSFERASE MTMB1
    Chains: A
    EC Number: 2.1.1.-
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 2208
    Strain: MS
    Synonym: MMA METHYLTRANSFERASE 1, MMAMT 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1BG31Ligand/Ion3-METHYL-5-SULFO-PYRROLIDINE-2-CARBOXYLIC ACID
2SO410Ligand/IonSULFATE ION
Biological Unit 1 (2, 66)
No.NameCountTypeFull Name
1BG36Ligand/Ion3-METHYL-5-SULFO-PYRROLIDINE-2-CARBOXYLIC ACID
2SO460Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:303 , HOH A:651 , HOH A:682 , HOH A:757 , HOH A:761BINDING SITE FOR RESIDUE SO4 A 503
02AC2SOFTWAREGLU A:343 , MET A:344 , HOH A:679BINDING SITE FOR RESIDUE SO4 A 504
03AC3SOFTWAREGLU A:137 , THR A:162 , SER A:163 , LYS A:432 , HOH A:571 , HOH A:640 , HOH A:729BINDING SITE FOR RESIDUE SO4 A 505
04AC4SOFTWAREARG A:4 , THR A:437 , GLU A:438 , HOH A:892 , HOH A:896BINDING SITE FOR RESIDUE SO4 A 501
05AC5SOFTWAREGLU A:397 , ILE A:398 , SER A:399 , HOH A:767BINDING SITE FOR RESIDUE SO4 A 506
06AC6SOFTWAREPRO A:420 , ALA A:421 , HOH A:756BINDING SITE FOR RESIDUE SO4 A 507
07AC7SOFTWARELYS A:167 , SER A:168 , HOH A:711 , HOH A:973BINDING SITE FOR RESIDUE SO4 A 508
08AC8SOFTWAREPHE A:47 , LYS A:48 , GLY A:49 , ILE A:271 , GLU A:272 , MET A:313 , HOH A:736 , HOH A:810BINDING SITE FOR RESIDUE SO4 A 509
09AC9SOFTWAREGLN A:24 , HIS A:81 , HOH A:669BINDING SITE FOR RESIDUE SO4 A 510
10BC1SOFTWARELYS A:100 , ALA A:122 , LYS A:123 , ARG A:391 , HOH A:937 , HOH A:946BINDING SITE FOR RESIDUE SO4 A 502
11BC2SOFTWARETHR A:131 , GLY A:132 , VAL A:157 , LYS A:202 , GLU A:205 , GLU A:229 , GLU A:259 , MET A:261 , LEU A:295 , GLN A:333 , TYR A:335 , SER A:365 , HOH A:751 , HOH A:779 , HOH A:914 , HOH A:980BINDING SITE FOR RESIDUE BG3 A 511

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:341 -A:428

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:203 -Pro A:204
2Asn A:234 -Glu A:235
3Gly A:366 -Val A:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTMB1_METBA_001 *A36SMTMB1_METBA  ---  ---AA36S
2UniProtVAR_MTMB1_METBA_002 *G219AMTMB1_METBA  ---  ---AT220A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_MTMB1_METBA_001 *A36SMTMB1_METBA  ---  ---AA36S
2UniProtVAR_MTMB1_METBA_002 *G219AMTMB1_METBA  ---  ---AT220A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TV4)

(-) Exons   (0, 0)

(no "Exon" information available for 1TV4)

(-) 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:457
 aligned with MTMB1_METBA | O30642 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:457
                                                                                                                                                                                                                                   202                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                 201 |                                                                                                                                                                                                                                                               
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 |     210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       
          MTMB1_METBA     2 TFRKSFDCYDFYDRAKVGEKCTQDDWDLMKIPMKAMELKQKYGLDFKGEFIPTDKDMMEKLFKAGFEMLLECGIYCTDTHRIVKYTEDEIWDAINNVQKEFVLGTGRDAVNVRKRSVGDKAKPIVQGGPTGSPISEDVFMPVHMSYALEKEVDTIVNGVMTSVRGKSPIPKSPYEVLAAKTETRLIKNACAMAGRPGMGV-GPETSLSAQGNISADCTGGMTCTDSHEVSQLNELKIDLDAISVIAHYKGNSDIIMDEQMPIFGGYAGGIEETTIVDVATHINAVLMSSASWHLDGPVHIRWGSTNTRETLMIAGWACATISEFTDILSGNQYYPCAGPCTEMCLLEASAQSITDTASGREILSGVASAKGVVTDKTTGMEARMMGEVARATAGVEISEVNVILDKLVSLYEKNYASAPAGKTFQECYDVKTVTPTEEYMQVYDGARKKLEDLGLVF 457
               SCOP domains d1tv4a_ A: Monomethylamine methyltransferase MtmB                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhheee....eee..hhhhhhhhhh.....eee.hhhhheee...........eeee.....eehhhhhhhhhhhhhh.....eee..ee...........hhhhhhhhhhhhhhhhhhhhhh......eee.....hhhhhhh...........eeeee.....eehhhhhhhhhhhhhh..eeeee...ee.....hhhhhhhhhhhhhhhhhhhh...eeee..ee.......hhhhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh............hhhhhee....eehhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tv4 A   2 TFRKSFDCYDFYDRAKVGEKCTQDDWDLMKIPMKAMELKQKYGLDFKGEFIPTDKDMMEKLFKAGFEMLLECGIYCTDTHRIVKYTEDEIWDAINNVQKEFVLGTGRDAVNVRKRSVGDKAKPIVQGGPTGSPISEDVFMPVHMSYALEKEVDTIVNGVMTSVRGKSPIPKSPYEVLAAKTETRLIKNACAMAGRPGMGVKGPETSLSAQGNISADCTGGMTCTDSHEVSQLNELKIDLDAISVIAHYKGNSDIIMDEQMPIFGGYAGGIEETTIVDVATHINAVLMSSASWHLDGPVHIRWGSTNTRETLMIAGWACATISEFTDILSGNQYYPCAGPCTEMCLLEASAQSITDTASGREILSGVASAKGVVTDKTTGMEARMMGEVARATAGVEISEVNVILDKLVSLYEKNYASAPAGKTFQECYDVKTVTPTEEYMQVYDGARKKLEDLGLVF 458
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TV4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TV4)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (MTMB1_METBA | O30642)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0043852    monomethylamine methyltransferase activity    Catalysis of the reaction: monomethylamine + a monomethylamine corrinoid protein = a methylated monomethylamine corrinoid protein + NH3.
    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:0015948    methanogenesis    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

 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
    BG3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:234 - Glu A:235   [ RasMol ]  
    Gly A:203 - Pro A:204   [ RasMol ]  
    Gly A:366 - Val A:367   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1tv4
    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
  MTMB1_METBA | O30642
    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)
  2.1.1.-
    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
  MTMB1_METBA | O30642
    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
        MTMB1_METBA | O30642: 1l2q 1nth 1tv2 1tv3

(-) Related Entries Specified in the PDB File

1l2q THE SAME PROTEIN WITHOUT SULFITE AND CRYSTALLIZED IN DIFFERENT CONDITION
1nth THE SAME PRETEIN WITHOUT SULFITE