2AVN - JenaLib

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Title :   CRYSTAL STRUCTURE OF A UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE-RELATED PROTEIN (TM1389) FROM THERMOTOGA MARITIMA MSB8 AT 2.35 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   30 Aug 05 (Deposition) - 18 Oct 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Ubiquinone/Menaquinone Biosynthesis Methyltransferase-Related Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Ubiquinone/Menaquinone Biosynthesis Methyltransferase-Related Protein (Tm1389) From Thermotoga Maritima At 2. 35 A Resolution
To Be Published
PubMed: search

Molecule 1 - UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE- RELATED PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	HK100
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM1389
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	243274
	Strain	:	MSB8

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	SAI	2	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Biological Unit 1 (3, 13)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	SAI	2	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Biological Unit 2 (3, 26)

No.	Name	Count	Type	Full Name
1	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	SAI	4	Ligand/Ion	S-ADENOSYL-L-HOMOSELENOCYSTEINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:210 , ARG A:214 , HOH A:1303 , HOH A:1330 , ALA B:155 , TRP B:156	BINDING SITE FOR RESIDUE PO4 A 249
2	AC2	SOFTWARE	SER A:5 , TYR A:9 , TYR A:16 , GLY A:50 , GLY A:51 , GLY A:52 , ASP A:71 , PRO A:72 , SER A:73 , LYS A:92 , ALA A:93 , GLU A:94 , LEU A:109 , GLY A:110 , VAL A:112 , TYR A:115 , HOH A:1305 , HOH A:1308 , HOH A:1318 , HOH A:1379 , HOH A:1380	BINDING SITE FOR RESIDUE SAI A 1300
3	AC3	SOFTWARE	SER B:5 , TYR B:9 , TYR B:16 , GLY B:50 , GLY B:51 , GLY B:52 , ASP B:71 , PRO B:72 , SER B:73 , MSE B:76 , LYS B:92 , ALA B:93 , GLU B:94 , LEU B:109 , GLY B:110 , VAL B:112 , TYR B:115 , HOH B:2307 , HOH B:2314 , HOH B:2353 , HOH B:2365	BINDING SITE FOR RESIDUE SAI B 2300

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

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

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

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

(no "Exon" information available for 2AVN)

Asymmetric Unit

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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:247
 aligned with Q9X1A9_THEMA | Q9X1A9 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                             1                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       
         Q9X1A9_THEMA     - -MKLRSWEFYDRIARAYDSMYETPKWKLYHRLIGSFLEEYLKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEMLEVAREKGVKNVVEAKAEDLPFPSGAFEAVLALGDVLSYVENKDKAFSEIRRVLVPDGLLIATVDNFYTFLQQMIEKDAWDQITRFLKTQTTSVGTTLFSFNSYAFKPEDLDSLEGFETVDIRGIGVMEYPDERISEREETIFRLEQELSRDRNIIWKADHIFFVLKKKR 246
               SCOP domains -d2avna1 A:1-246 Hypothetical methyltransferase TM1389                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhh...eeeeee.hhhhhhhhhhhh...eee............eeeeee..hhhhhh.hhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhh.hhhhhhhhhhhheeeee...eeeeee..hhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avn A   0 HmKLRSWEFYDRIARAYDSmYETPKWKLYHRLIGSFLEEYLKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEmLEVAREKGVKNVVEAKAEDLPFPSGAFEAVLALGDVLSYVENKDKAFSEIRRVLVPDGLLIATVDNFYTFLQQmIEKDAWDQITRFLKTQTTSVGTTLFSFNSYAFKPEDLDSLEGFETVDIRGIGVmEYPDERISEREETIFRLEQELSRDRNIIWKADHIFFVLKKKR 246
                             |       9        19        29        39        49        59        69      | 79        89        99       109       119       129       139       149|      159       169       179       189       199    |  209       219       229       239       
                             |                19-MSE                                                   76-MSE                                                                   150-MSE                                               204-MSE                                      
                             1-MSE

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q9X1A9_THEMA | Q9X1A9 from UniProtKB/TrEMBL  Length:248

    Alignment length:247
                             1                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       
         Q9X1A9_THEMA     - -MKLRSWEFYDRIARAYDSMYETPKWKLYHRLIGSFLEEYLKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEMLEVAREKGVKNVVEAKAEDLPFPSGAFEAVLALGDVLSYVENKDKAFSEIRRVLVPDGLLIATVDNFYTFLQQMIEKDAWDQITRFLKTQTTSVGTTLFSFNSYAFKPEDLDSLEGFETVDIRGIGVMEYPDERISEREETIFRLEQELSRDRNIIWKADHIFFVLKKKR 246
               SCOP domains d2avnb_ B: Hypothetical methyltransferase TM1389                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeee..hhhhhhhhhhhh...ee.............eeeeee..hhhhhh.hhhhhhhhhhhheeeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhheeeee...eeeeee..hhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh...hhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2avn B   0 HmKLRSWEFYDRIARAYDSmYETPKWKLYHRLIGSFLEEYLKNPCRVLDLGGGTGKWSLFLQERGFEVVLVDPSKEmLEVAREKGVKNVVEAKAEDLPFPSGAFEAVLALGDVLSYVENKDKAFSEIRRVLVPDGLLIATVDNFYTFLQQmIEKDAWDQITRFLKTQTTSVGTTLFSFNSYAFKPEDLDSLEGFETVDIRGIGVmEYPDERISEREETIFRLEQELSRDRNIIWKADHIFFVLKKKR 246
                             |       9        19        29        39        49        59        69      | 79        89        99       109       119       129       139       149|      159       169       179       189       199    |  209       219       229       239       
                             1-MSE            19-MSE                                                   76-MSE                                                                   150-MSE                                               204-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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

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

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: UbiE/COQ5-like (7)

Protein domain: Hypothetical methyltransferase TM1389 (1)

Thermotoga maritima [TaxId: 2336] (1)

1a	d2avna1	A:1-246
1b	d2avnb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9X1A9_THEMA | Q9X1A9)

molecular function
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.

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