1ARO - JenaLib

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Title :   T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME

Authors :   T. Steitz, D. Jeruzalmi

Date :   08 Aug 97 (Deposition) - 21 Oct 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : L,P

Keywords :   Transcription, Dna-Directed Rna Polymerase, Hydrolase, Glycosidase, Complex (Polymerase/Hydrolase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Jeruzalmi, T. A. Steitz
Structure Of T7 Rna Polymerase Complexed To The Transcriptional Inhibitor T7 Lysozyme.
Embo J. V. 17 4101 1998
PubMed-ID: 9670025 | Reference-DOI: 10.1093/EMBOJ/17.14.4101
(for further references see the PDB file header)

Molecule 1 - T7 RNA POLYMERASE
	Chains	:	P
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Gene	:	T7
	Expression System Plasmid	:	T7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	T7
	Gene	:	T7
	Mutation	:	YES
	Organism Scientific	:	ENTEROBACTERIA PHAGE T7
	Organism Taxid	:	10760

Molecule 2 - T7 LYSOZYME
	Chains	:	L
	EC Number	:	3.5.1.28
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Gene	:	T7
	Expression System Plasmid	:	T7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	T7
	Gene	:	T7
	Organism Scientific	:	ENTEROBACTERIA PHAGE T7
	Organism Taxid	:	10760
	Synonym	:	N-ACETYLMURAMOYL-L-ALANINE AMIDASE

		1	2
Asymmetric/Biological Unit	:	L	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 7)

No.	Name	Count	Type	Full Name
1	HG	7	Ligand/Ion	MERCURY (II) ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS L:1018 , SER L:1019 , CYS L:1130	BINDING SITE FOR RESIDUE HG L 903
2	AC2	SOFTWARE	CYS P:125 , ALA P:140	BINDING SITE FOR RESIDUE HG P 904
3	AC3	SOFTWARE	GLU P:517 , TYR P:528 , CYS P:530	BINDING SITE FOR RESIDUE HG P 905
4	AC4	SOFTWARE	CYS P:467 , CYS P:510	BINDING SITE FOR RESIDUE HG P 906
5	AC5	SOFTWARE	MET P:313	BINDING SITE FOR RESIDUE HG P 907
6	AC6	SOFTWARE	MET P:401	BINDING SITE FOR RESIDUE HG P 908
7	AC7	SOFTWARE	SER P:539 , CYS P:540	BINDING SITE FOR RESIDUE HG P 909

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

Asymmetric/Biological Unit

No.	Residues
1	Cys L:1130	-	Pro L:1131

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNA_POL_PHAGE_1	PS00900	Bacteriophage-type RNA polymerase family active site signature 1.	RPOL_BPT7	533-544	1	P:533-544
2	RNA_POL_PHAGE_2	PS00489	Bacteriophage-type RNA polymerase family active site signature 2.	RPOL_BPT7	625-639	1	P:625-639

(no "Exon" information available for 1ARO)

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 L from PDB  Type:PROTEIN  Length:149
 aligned with ENLYS_BPT7 | P00806 from UniProtKB/Swiss-Prot  Length:151

    Alignment length:149
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142         
          ENLYS_BPT7      3 RVQFKQRESTDAIFVHCSATKPSQNVGVREIRQWHKEQGWLDVGYHFIIKRDGTVEAGRDEMAVGSHAKGYNHNSIGVCLVGGIDDKGKFDANFTPAQMQSLRSLLVTLLAKYEGAVLRAHHEVAPKACPSFDLKRWWEKNELVTSDRG  151
               SCOP domains d1arol_ L: Bacteriophage T7 lysozyme (Zn amidase)                                                                                                     SCOP domains
               CATH domains 1aroL00 L:1002-1150 Lysozyme                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee..........hhhhhhhhhh.........eee.....eee..............hhheeeeee...............hhhhhhhhhhhhhhhhh....eeeehhh..........hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1aro L 1002 RVQFKQRESTDAIFVHCSATKPSQNVGVREIRQWHKEQGWLDVGYHFIIKRDGTVEAGRDEMAVGSHAKGYNHNSIGVCLVGGIDDKGKFDANFTPAQMQSLRSLLVTLLAKYEGAVLRAHHEVAPKACPSFDLKRWWEKNELVTSDRG 1150
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141

Chain P from PDB  Type:PROTEIN  Length:774
 aligned with RPOL_BPT7 | P00573 from UniProtKB/Swiss-Prot  Length:883

    Alignment length:872
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877  
           RPOL_BPT7      8 KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNVEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQNAGVVGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESD  879
               SCOP domains d1arop_ P: T7 RNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1aroP01 P:8-325 T7 RNA polymerase, domain 1                                                                                                                                                                                                                                                                                   1aroP02 P:326-411                                                                     ---------1aroP03                      1aroP04 P:450-527  [code=1.10.287.280, no name defined]                       1aroP03                   1aroP05 P:554-784 5' to 3' exonuclea                      se, C-terminal subdomain                                                                                                                                                     1aroP03 P:421-449,P:528-553,P:785-879  [code=3.30.70.370, no name defined]                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhh.-------------....hhhhhhhhhhhhhhhh..........hhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh....-----------------........................hhhhhhhhhhhhhhhhhh..........-------.......hhhhhhhhh...hhhh......................................hhhhhh......hhhhhhhhhhhh..eee.hhhhhhhhhh...---------------------------------------.....hhhhhhhhhhhhhhhhhhh..........eee.....eee.........hhhhhheee......hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..........hhh....hhhhhhhhhhhhhhhh....................hhhhhh..hhhhhhh..........hhhhhhhhhhhhhhhhh...----------------------.......hhhhh...................hhhhhhhhhhh..hhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..................eeee.....eeee.................................hhhhhh.hhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....................hhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RNA_POL_PHAG--------------------------------------------------------------------------------RNA_POL_PHAGE_2------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1aro P    8 KNDFSDIELAAIPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQL-------------LITTLLPKMIARINDWFEEVKAKRGKRPTAFQFLQEIKPEAVAYITIKTTLACLTSADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKK-----------------FMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQN-------SETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHSKKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKW---------------------------------------VYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVSMFNPQGNDMTKGLLTLAKGKPIGKEGYYWLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLENTWWAEQDSPFCFLAFCFEYAGVQHHGLSYNCSLPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAING----------------------GTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEAMNWLKSAAKLLAAEVKDKKTGEILRKRSAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESSDVLADFYDQFADQLHESQLDKMPALPAKGNLNLRDILESD  879
                                    17        27        37        47        57 |       -     |  77        87        97       107       117       127       137       147       157      |  -         -    |  187       197       207       217       227     |   -   |   247       257       267       277       287       297       307       317       327       337      |  -         -         -         -      |387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587 |       -         -    |  617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877  
                                                                              59            73                                                                                        164               182                                                233     241                                                                                                    344                                     384                                                                                                                                                                                                          589                    612

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 '\|'

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (ENLYS_BPT7 | P00806)

molecular function
	GO:0008745	N-acetylmuramoyl-L-alanine amidase activity	Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	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:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0019076	viral release from host cell	The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
cellular component
	GO:0030430	host cell cytoplasm	The cytoplasm of a host cell.

Chain P (RPOL_BPT7 | P00573)

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: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:0039695	DNA-templated viral transcription	A transcription process that uses a viral DNA as a template.
	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
		Cys L:1130 - Pro L:1131	[ RasMol ]

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	RPOL_BPT7 \| P00573	:	1cez 1h38 1msw 1qln 1s0v 1s76 1s77 2pi4 2pi5 3e2e 3e3j 4rnp

(no "Related Entries Specified in the PDB File" available for 1ARO)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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