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Title :   CRYSTAL STRUCTURE OF TA1416,DNA-DIRECTED RNA POLYMERASE SUBUNIT L, FROM THERMOPLASMA ACIDOPHILUM

Authors :   Y. Kim, A. Joachimiak, E. Evdokimova, A. Savchenko, A. Edwards, Midwes For Structural Genomics (Mcsg)

Date :   09 Oct 04 (Deposition) - 23 Nov 04 (Release) - 26 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Structural Genomics, Dna-Directed Rna Polymerase, Thermoplasma Acidophilum, Protein Structure Initiative, Mcsg, Midwest Center For Structural Genomics, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, A. Joachimiak, E. Evdokimova, A. Savchenko, A. Edwards
Crystal Structure Of Ta1416, Dna-Directed Rna Polymerase Subunit L, From Thermoplasma Acidophilum
To Be Published
PubMed: search

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT L
	Chains	:	A, B, C, D
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector	:	MODIFIED PET15B
	Expression System Vector Type	:	PLASMID
	Gene	:	RPOL
	Organism Scientific	:	THERMOPLASMA ACIDOPHILUM
	Organism Taxid	:	2303
	Synonym	:	TA1416

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	FMT	1	Ligand/Ion	FORMIC ACID
3	SCN	3	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:77	BINDING SITE FOR RESIDUE SCN B 601
2	AC2	SOFTWARE	TYR C:87 , TYR D:87	BINDING SITE FOR RESIDUE SCN C 602
3	AC3	SOFTWARE	HIS A:55 , PRO A:56 , VAL A:57 , ILE A:58 , ARG C:50 , TYR C:51	BINDING SITE FOR RESIDUE SCN A 603
4	AC4	SOFTWARE	ARG A:50 , TYR A:52 , ILE A:53 , HOH A:673 , ILE C:53 , LYS C:54 , PRO C:56	BINDING SITE FOR RESIDUE FMT C 604
5	AC5	SOFTWARE	ASP A:29 , GLU B:38 , GLU B:39 , LYS B:42	BINDING SITE FOR RESIDUE ACY B 605

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

Asymmetric/Biological Unit

No.	Residues
1	His B:55	-	Pro B:56
2	His D:55	-	Pro D:56

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNA_POL_L_13KD	PS01154	RNA polymerases L / 13 to 16 Kd subunits signature.	RPOL_THEAC	25-56	4	A:25-56 B:25-56 C:25-56 D:25-56

(no "Exon" information available for 1XPP)

Asymmetric/Biological 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:99
 aligned with RPOL_THEAC | Q9HIC5 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:99
                                    16        26        36        46        56        66        76        86        96         
           RPOL_THEAC     7 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDH 105
               SCOP domains d1xppa_ A: DNA-directed RNA polymerase subunit L, RpoL                                              SCOP domains
               CATH domains 1xppA00 A:7-105  [code=3.30.1360.10, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee..hhhhhhhhhhhhh....eeeeeee.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------RNA_POL_L_13KD  PDB: A:25-56    ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1xpp A   7 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDH 105
                                    16        26        36        46        56        66        76        86        96

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with RPOL_THEAC | Q9HIC5 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:98
                                    17        27        37        47        57        67        77        87        97        
           RPOL_THEAC     8 ESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDH 105
               SCOP domains d1xppb_ B: DNA-directed RNA polymerase subunit L, RpoL                                             SCOP domains
               CATH domains 1xppB00 B:8-105  [code=3.30.1360.10, no name defined]                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeee..hhhhhhhhhhhhh....eeeeeee.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------RNA_POL_L_13KD  PDB: B:25-56    ------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1xpp B   8 ESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDH 105
                                    17        27        37        47        57        67        77        87        97

Chain C from PDB  Type:PROTEIN  Length:99
 aligned with RPOL_THEAC | Q9HIC5 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:99
                                    16        26        36        46        56        66        76        86        96         
           RPOL_THEAC     7 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDH 105
               SCOP domains d1xppc_ C: DNA-directed RNA polymerase subunit L, RpoL                                              SCOP domains
               CATH domains 1xppC00 C:7-105  [code=3.30.1360.10, no name defined]                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee..hhhhhhhhhhhhh....eeeeeee.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------RNA_POL_L_13KD  PDB: C:25-56    ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1xpp C   7 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDH 105
                                    16        26        36        46        56        66        76        86        96

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with RPOL_THEAC | Q9HIC5 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:101
                                    16        26        36        46        56        66        76        86        96       106 
           RPOL_THEAC     7 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDHMI 107
               SCOP domains d1xppd_ D: DNA-directed RNA polymerase subunit L, RpoL                                                SCOP domains
               CATH domains 1xppD00 D:7-107  [code=3.30.1360.10, no name defined]                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee..hhhhhhhhhhhhh....eeeeeee.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------RNA_POL_L_13KD  PDB: D:25-56    --------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 1xpp D   7 AESSLRVISKEKNSITVEMINYDNTLLRTLVEEILKDDQVDEARYYIKHPVIDNPQIYVRVKSGKPQSAIKRAVRKLSKLYEDLGTQFQKEFQRYESDHMI 107
                                    16        26        36        46        56        66        76        86        96       106

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: DCoH-like (107)

Superfamily: RBP11-like subunits of RNA polymerase (76)

Family: RBP11/RpoL (31)

Protein domain: DNA-directed RNA polymerase subunit L, RpoL (1)

Thermoplasma acidophilum [TaxId: 2303] (1)

1a	d1xppa_	A:
1b	d1xppb_	B:
1c	d1xppc_	C:
1d	d1xppd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Gyrase A; domain 2 (166)

Homologous Superfamily: [code=3.30.1360.10, no name defined] (72)

Thermoplasma acidophilum. Organism_taxid: 2303. (1)

1a	1xppD00	D:7-107
1b	1xppA00	A:7-105
1c	1xppC00	C:7-105
1d	1xppB00	B:8-105

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (RPOL_THEAC | Q9HIC5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		His B:55 - Pro B:56	[ RasMol ]
		His D:55 - Pro D:56	[ RasMol ]

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	1xpp
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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