3NM6 - JenaLib

Title :   HELICOBACTER PYLORI MTAN COMPLEXED WITH ADENINE AND TRIS

Authors :   D. R. Ronning, N. M. Iacopelli

Date :   21 Jun 10 (Deposition) - 24 Nov 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym. Unit : B
Biol. Unit 1: B  (2x)

Keywords :   Nucleosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. R. Ronning, N. M. Iacopelli, V. Mishra
Enzyme-Ligand Interactions That Drive Active Site Rearrangements In The Helicobacter Pylori 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase.
Protein Sci. V. 19 2498 2010
PubMed-ID: 20954236 | Reference-DOI: 10.1002/PRO.524

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL B:78 , ALA B:79 , GLY B:80 , PHE B:153 , VAL B:154 , VAL B:172 , GLU B:173 , MET B:174 , SER B:197 , ASP B:198 , ALA B:200 , TRS B:232	BINDING SITE FOR RESIDUE ADE B 231
2	AC2	SOFTWARE	ALA B:9 , MET B:10 , GLU B:13 , VAL B:78 , GLU B:173 , MET B:174 , GLU B:175 , ARG B:194 , PHE B:208 , ADE B:231	BINDING SITE FOR RESIDUE TRS B 232
3	AC3	SOFTWARE	SER B:126 , LEU B:127 , LEU B:130 , LEU B:230 , HOH B:346 , HOH B:383	BINDING SITE FOR RESIDUE EDO B 1001
4	AC4	SOFTWARE	ASN B:33 , VAL B:34 , TYR B:49 , HOH B:260 , HOH B:341	BINDING SITE FOR RESIDUE EDO B 1002
5	AC5	SOFTWARE	PHE B:68 , HOH B:387	BINDING SITE FOR RESIDUE EDO B 1003
6	AC6	SOFTWARE	GLU B:137 , GLU B:229	BINDING SITE FOR RESIDUE EDO B 1004

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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 B from PDB  Type:PROTEIN  Length:229
 aligned with MQMTN_HELPJ | Q9ZMY2 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
          MQMTN_HELPJ     2 QKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 230
               SCOP domains d3nm6b_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhh...eeeee..eeeeeeee..eeeeeee...hhhhhhhhhhhhhhhhh..eeeeeeeeee.........eeeeeeeee....hhhhh...........eee.hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhh..eee.hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nm6 B   2 QKIGILGAMREEITPILELFGVDFEEIPLGGNVFHKGVYHNKEIIVAYSKIGKVHSTLTTTSMILAFGVQKVLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHPLGFIPESAIFIETSGSLNALAKKIANEQHIALKEGVIASGDQFVHSKERKEFLVSEFKASAVEMEGASVAFVCQKFGVPCCVLRSISDNADEKAGMSFDEFLEKSAHTSAKFLKSMVDEL 230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain B (MQMTN_HELPJ | Q9ZMY2)

molecular function
	GO:0008782	adenosylhomocysteine nucleosidase activity	Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenine + S-D-ribosyl-L-homocysteine.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008930	methylthioadenosine nucleosidase activity	Catalysis of the reaction: methylthioadenosine + H2O = adenine + 5-methylthio-D-ribose.
biological process
	GO:0019509	L-methionine salvage from methylthioadenosine	The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009234	menaquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
	GO:0009086	methionine biosynthetic process	The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
	GO:0009164	nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0009116	nucleoside metabolic process	The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).

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
		ADE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRS	[ 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 3nm6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3nm6
		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
	MQMTN_HELPJ \| Q9ZMY2
		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)
	3.2.2.9
		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

Description