1NXJ - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF RV3853 FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   J. M. Johnston, V. L. Arcus, E. N. Baker, Tb Structural Genomics Consortium (Tbsgc)

Date :   10 Feb 03 (Deposition) - 29 Jul 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)
Biol. Unit 3: C  (3x)

Keywords :   Beta/Beta/Alpha Domain, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Johnston, V. L. Arcus, C. J. Morton, M. W. Parker, E. N. Baker
Crystal Structure Of A Putative Methyltransferase From Mycobacterium Tuberculosis: Misannotation Of A Genome Clarified By Protein Structural Analysis
J. Bacteriol. V. 185 4057 2003
PubMed-ID: 12837779 | Reference-DOI: 10.1128/JB.185.14.4057-4065.2003
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B, C
	EC Number	:	2.1.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEX HTA
	Expression System Strain	:	BL21(DE3) PRI592
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MENG
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (3x)	:	A
Biological Unit 2 (3x)	:		B
Biological Unit 3 (3x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GLV	3	Ligand/Ion	GLYOXYLIC ACID
2	TLA	3	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GLV	3	Ligand/Ion	GLYOXYLIC ACID
2	TLA	3	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	GLV	3	Ligand/Ion	GLYOXYLIC ACID
2	TLA	3	Ligand/Ion	L(+)-TARTARIC ACID

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	GLV	3	Ligand/Ion	GLYOXYLIC ACID
2	TLA	3	Ligand/Ion	L(+)-TARTARIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:25 , PHE A:26 , ARG A:27 , THR A:117 , ASP A:151 , HOH A:751 , HOH A:802	BINDING SITE FOR RESIDUE GLV A 741
2	AC2	SOFTWARE	LEU B:24 , GLN B:25 , PHE B:26 , ARG B:27 , THR B:117 , ASP B:151 , HOH B:755	BINDING SITE FOR RESIDUE GLV B 742
3	AC3	SOFTWARE	GLN C:25 , PHE C:26 , ARG C:27 , THR C:117 , ASP C:151 , HOH C:759 , HOH C:771	BINDING SITE FOR RESIDUE GLV C 743
4	AC4	SOFTWARE	ASN A:48 , ALA A:75 , GLY A:78 , ASP A:79 , VAL A:80 , ILE A:81 , ARG A:100 , LYS A:121 , SER A:122 , LYS A:124 , HOH A:777	BINDING SITE FOR RESIDUE TLA A 391
5	AC5	SOFTWARE	ASN B:48 , ALA B:75 , GLY B:78 , ASP B:79 , VAL B:80 , ILE B:81 , ARG B:100 , LYS B:121 , SER B:122 , LYS B:124 , HOH B:777	BINDING SITE FOR RESIDUE TLA B 392
6	AC6	SOFTWARE	ASN C:48 , ALA C:75 , GLY C:78 , ASP C:79 , VAL C:80 , ILE C:81 , ARG C:100 , LYS C:121 , SER C:122 , LYS C:124 , HOH C:821	BINDING SITE FOR RESIDUE TLA C 393

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

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

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

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

(no "Exon" information available for 1NXJ)

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:156
 aligned with RRAAH_MYCTO | P9WGY2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
          RRAAH_MYCTO     2 AISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
               SCOP domains d1nxja_ A: Hypothetical protein Rv3853                                                                                                                       SCOP domains
               CATH domains 1nxjA00 A:2-157  [code=3.50.30.40, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh...ee.....ee......eeeeeeeee....hhhhhhhhhh.....eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeee....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nxj A   2 AISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain A from PDB  Type:PROTEIN  Length:156
 aligned with RRAAH_MYCTU | P9WGY3 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
          RRAAH_MYCTU     2 AISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
               SCOP domains d1nxja_ A: Hypothetical protein Rv3853                                                                                                                       SCOP domains
               CATH domains 1nxjA00 A:2-157  [code=3.50.30.40, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh...ee.....ee......eeeeeeeee....hhhhhhhhhh.....eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeee....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nxj A   2 AISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with RRAAH_MYCTO | P9WGY2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
          RRAAH_MYCTO     3 ISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
               SCOP domains d1nxjb_ B: Hypothetical protein Rv3853                                                                                                                      SCOP domains
               CATH domains 1nxjB00 B:3-157  [code=3.50.30.40, no name defined]                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..........ee......eeeeeeeee....hhhhhhhhh......eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeee....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxj B   3 ISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with RRAAH_MYCTU | P9WGY3 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152     
          RRAAH_MYCTU     3 ISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
               SCOP domains d1nxjb_ B: Hypothetical protein Rv3853                                                                                                                      SCOP domains
               CATH domains 1nxjB00 B:3-157  [code=3.50.30.40, no name defined]                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh..........ee......eeeeeeeee....hhhhhhhhh......eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeee....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxj B   3 ISFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with RRAAH_MYCTO | P9WGY2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
          RRAAH_MYCTO     4 SFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
               SCOP domains d1nxjc_ C: Hypothetical protein Rv3853                                                                                                                     SCOP domains
               CATH domains 1nxjC00 C:4-157  [code=3.50.30.40, no name defined]                                                                                                        CATH domains
           Pfam domains (1) Methyltransf_6-1nxjC01 C:4-156                                                                                                                           - Pfam domains (1)
           Pfam domains (2) Methyltransf_6-1nxjC02 C:4-156                                                                                                                           - Pfam domains (2)
           Pfam domains (3) Methyltransf_6-1nxjC03 C:4-156                                                                                                                           - Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhh...ee.....ee......eeeeeeeee....hhhhhhhhh......eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeee....eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxj C   4 SFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

Chain C from PDB  Type:PROTEIN  Length:154
 aligned with RRAAH_MYCTU | P9WGY3 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:154
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153    
          RRAAH_MYCTU     4 SFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
               SCOP domains d1nxjc_ C: Hypothetical protein Rv3853                                                                                                                     SCOP domains
               CATH domains 1nxjC00 C:4-157  [code=3.50.30.40, no name defined]                                                                                                        CATH domains
           Pfam domains (1) Methyltransf_6-1nxjC01 C:4-156                                                                                                                           - Pfam domains (1)
           Pfam domains (2) Methyltransf_6-1nxjC02 C:4-156                                                                                                                           - Pfam domains (2)
           Pfam domains (3) Methyltransf_6-1nxjC03 C:4-156                                                                                                                           - Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhh...ee.....ee......eeeeeeeee....hhhhhhhhh......eeeee.......eeehhhhhhhhhhh...eeeeeeee.hhhhhh....eeeeeee...........ee...eee..eee....eeee....eeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxj C   4 SFRPTADLVDDIGPDVRSCDLQFRQFGGRSQFAGPISTVRCFQDNALLKSVLSQPSAGGVLVIDGAGSLHTALVGDVIAELARSTGWTGLIVHGAVRDAAALRGIDIGIKALGTNPRKSTKTGAGERDVEITLGGVTFVPGDIAYSDDDGIIVV 157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153

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: The swivelling beta/beta/alpha domain (136)

Superfamily: RraA-like (6)

Family: RraA-like (5)

Protein domain: Hypothetical protein Rv3853 (1)

Mycobacterium tuberculosis [TaxId: 1773] (1)

1a	d1nxja_	A:
1b	d1nxjb_	B:
1c	d1nxjc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: Glucose Oxidase; domain 1 (52)

Homologous Superfamily: [code=3.50.30.40, no name defined] (6)

Mycobacterium tuberculosis. Organism_taxid: 1773. (1)

1a	1nxjA00	A:2-157
1b	1nxjB00	B:3-157
1c	1nxjC00	C:4-157

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Methyltransf_6] (5)

Family: Methyltransf_6 (5)

Mycobacterium tuberculosis (1)

1a	Methyltransf_6-1nxjC01	C:4-156
1b	Methyltransf_6-1nxjC02	C:4-156
1c	Methyltransf_6-1nxjC03	C:4-156

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RRAAH_MYCTU | P9WGY3)

molecular function
	GO:0047443	4-hydroxy-4-methyl-2-oxoglutarate aldolase activity	Catalysis of the reaction: 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate.
	GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008948	oxaloacetate decarboxylase activity	Catalysis of the reaction: oxaloacetate = pyruvate + CO2.
	GO:0008428	ribonuclease inhibitor activity	Stops, prevents or reduces the activity of a ribonuclease, any enzyme that catalyzes the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	GO:0051252	regulation of RNA metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.

Chain A,B,C (RRAAH_MYCTO | P9WGY2)

molecular function
	GO:0047443	4-hydroxy-4-methyl-2-oxoglutarate aldolase activity	Catalysis of the reaction: 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008948	oxaloacetate decarboxylase activity	Catalysis of the reaction: oxaloacetate = pyruvate + CO2.
	GO:0008428	ribonuclease inhibitor activity	Stops, prevents or reduces the activity of a ribonuclease, any enzyme that catalyzes the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	GO:0051252	regulation of RNA metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.

Asymmetric Unit
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