1NTH - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE METHANOSARCINA BARKERI MONOMETHYLAMINE METHYLTRANSFERASE (MTMB)

Authors :   B. Hao, W. Gong, T. K. Ferguson, C. M. James, J. A. Krzycki, M. K. Chan

Date :   30 Jan 03 (Deposition) - 04 Feb 03 (Release) - 13 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Tim Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Hao, W. Gong, T. K. Ferguson, C. M. James, J. A. Krzycki, M. K. Chan
A New Uag-Encoded Residue In The Structure Of A Methanogen Methyltransferase
Science V. 296 1462 2002
PubMed-ID: 12029132 | Reference-DOI: 10.1126/SCIENCE.1069556

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PYL	1	Mod. Amino Acid

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	PYL	-1	Mod. Amino Acid

(no "Site" information available for 1NTH)

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

Asymmetric Unit

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

Asymmetric Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MTMB1_METBA_001 *	A	36	S	MTMB1_METBA	---	---	A	A	36	S
2	UniProt	VAR_MTMB1_METBA_002 *	G	219	A	MTMB1_METBA	---	---	A	T	220	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_MTMB1_METBA_001 *	A	36	S	MTMB1_METBA	---	---	A	A	36	S
2	UniProt	VAR_MTMB1_METBA_002 *	G	219	A	MTMB1_METBA	---	---	A	T	220	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 1NTH)

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 d1ntha_ A: Monomethylamine methyltransferase MtmB                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhheee....eee..hhhhhhhhhh....eeee.hhhhheeee..........eeee.....eehhhhhhhhhhhhhh.....eee..ee...........hhhhhhhhhhhhhhhhhhhhhh......eee.....hhhhhhh...........eeeee.....eehhhhhhhhhhhhhh..eeeee...ee.....hhhhhhhhhhhhhhhhhhhh...eeee..ee.......hhhhhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhh..eeee..hhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh............hhhhhee....eehhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nth A   2 TFRKSFDCYDFYDRAKVGEKCTQDDWDLMKIPMKAMELKQKYGLDFKGEFIPTDKDMMEKLFKAGFEMLLECGIYCTDTHRIVKYTEDEIWDAINNVQKEFVLGTGRDAVNVRKRSVGDKAKPIVQGGPTGSPISEDVFMPVHMSYALEKEVDTIVNGVMTSVRGKSPIPKSPYEVLAAKTETRLIKNACAMAGRPGMGVxGPETSLSAQGNISADCTGGMTCTDSHEVSQLNELKIDLDAISVIAHYKGNSDIIMDEQMPIFGGYAGGIEETTIVDVATHINAVLMSSASWHLDGPVHIRWGSTNTRETLMIAGWACATISEFTDILSGNQYYPCAGPCTEMCLLEASAQSITDTASGREILSGVASAKGVVTDKTTGMEARMMGEVARATAGVEISEVNVILDKLVSLYEKNYASAPAGKTFQECYDVKTVTPTEEYMQVYDGARKKLEDLGLVF 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       
                                                                                                                                                                                                                                  202-PYL

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Monomethylamine methyltransferase MtmB (5)

Family: Monomethylamine methyltransferase MtmB (5)

Protein domain: Monomethylamine methyltransferase MtmB (5)

Methanosarcina barkeri [TaxId: 2208] (5)

d1ntha_

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

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

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.

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
		PYL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1nth)

	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 ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 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)

Access by PDB/NDB ID
	1nth
		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

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)

UniProtKB/Swiss-Prot
	MTMB1_METBA \| O30642	:	1l2q 1tv2 1tv3 1tv4

1l2q	CRYSTAL STRUCTURE OF MTMB ((NH4)2SO4 FORM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File