1E3P - JenaLib

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Title :   TUNGSTATE DERIVATIVE OF STREPTOMYCES ANTIBIOTICUS PNPASE/ GPSI ENZYME

Authors :   M. F. Symmons, G. H. Jones, B. F. Luisi

Date :   20 Jun 00 (Deposition) - 03 Nov 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Polyribonucleotide Transferase, Atp-Gtp Diphosphotransferase Rna Processing, Rna Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. F. Symmons, G. H. Jones, B. F. Luisi
A Duplicated Fold Is The Structural Basis For Polynucleotide Phosphorylase Catalytic Activity, Processivity, And Regulation
Structure V. 8 1215 2000
PubMed-ID: 11080643 | Reference-DOI: 10.1016/S0969-2126(00)00521-9

Molecule 1 - GUANOSINE PENTAPHOSPHATE SYNTHETASE
	Cellular Location	:	CYTOPLASM
	Chains	:	A
	EC Number	:	2.7.7.8, 2.7.6.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Taxid	:	562
	Gene	:	GPSI
	Organism Scientific	:	STREPTOMYCES ANTIBIOTICUS
	Organism Taxid	:	1890
	Other Details	:	BIFUNCTIONAL ENZYME POLYRIBONUCLEOTIDE NUCLEOTIDYL TRANSFERASE, ATP-GTP DIPHOSPHOTRANSFERASE
	Other Details - Source	:	BIFUNCTIONAL ENZYME ISOLATED
	Strain	:	IMRU3720
	Synonym	:	POLYNUCLEOTIDE PHOSPHORYLASE, GUANOSINE PENTAPHOSPHATE SYNTHETASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 11)

No.	Name	Count	Type	Full Name
1	SO4	10	Ligand/Ion	SULFATE ION
2	WO4	1	Ligand/Ion	TUNGSTATE(VI)ION

Biological Unit 1 (2, 33)

No.	Name	Count	Type	Full Name
1	SO4	30	Ligand/Ion	SULFATE ION
2	WO4	3	Ligand/Ion	TUNGSTATE(VI)ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:84 , ARG A:86 , GLN A:388 , HOH A:2081	BINDING SITE FOR RESIDUE SO4 A 901
02	AC2	SOFTWARE	ILE A:569 , ASP A:570 , THR A:571	BINDING SITE FOR RESIDUE SO4 A 902
03	AC3	SOFTWARE	LYS A:421 , ARG A:422 , HOH A:2297	BINDING SITE FOR RESIDUE SO4 A 903
04	AC4	SOFTWARE	GLY A:415 , ARG A:416	BINDING SITE FOR RESIDUE SO4 A 904
05	AC5	SOFTWARE	SER A:54 , LYS A:55 , ASN A:56 , LYS A:58 , HOH A:2052	BINDING SITE FOR RESIDUE SO4 A 905
06	AC6	SOFTWARE	PHE A:64 , LYS A:112 , GLY A:113 , ARG A:115 , HOH A:2299	BINDING SITE FOR RESIDUE SO4 A 906
07	AC7	SOFTWARE	ARG A:160 , ASP A:183 , VAL A:185 , GLU A:202 , GLU A:204 , HOH A:2301	BINDING SITE FOR RESIDUE SO4 A 907
08	AC8	SOFTWARE	GLU A:207 , ARG A:397 , ARG A:399 , ARG A:442 , HOH A:2236 , HOH A:2302	BINDING SITE FOR RESIDUE SO4 A 908
09	AC9	SOFTWARE	HIS A:131 , LEU A:132 , TYR A:133 , LEU A:392 , SER A:393 , HOH A:2112 , HOH A:2303	BINDING SITE FOR RESIDUE SO4 A 909
10	BC1	SOFTWARE	ARG A:360	BINDING SITE FOR RESIDUE SO4 A 910
11	BC2	SOFTWARE	HIS A:427 , SER A:461 , THR A:462 , SER A:463 , LYS A:522 , HOH A:2305	BINDING SITE FOR RESIDUE WO4 A 911

(no "SS Bond" information available for 1E3P)

Asymmetric Unit

No.	Residues
1	Gly A:154	-	Pro A:155
2	Leu A:307	-	Pro A:308

(no "SAP(SNP)/Variant" information available for 1E3P)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PNP_STRAT	580-639	1	A:580-634
2	S1	PS50126	S1 domain profile.	PNP_STRAT	651-723	1	A:656-717

Biological Unit 1 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KH_TYPE_1	PS50084	Type-1 KH domain profile.	PNP_STRAT	580-639	3	A:580-634
2	S1	PS50126	S1 domain profile.	PNP_STRAT	651-723	3	A:656-717

(no "Exon" information available for 1E3P)

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:645
 aligned with PNP_STRAT | Q53597 from UniProtKB/Swiss-Prot  Length:740

    Alignment length:715
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712     
            PNP_STRAT     3 NETHYAEAVIDNGAFGTRTIRFETGRLAKQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPYGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTVQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEFPVPSSTTRTTSEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLLPEFEGREKEISAAYRPWPSSSSAERVIKEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKPYMHNYNFPPISVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTPDEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGK 717
               SCOP domains d1e3pa3 A:3-151 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4                                        d1e3pa6 A:152-262 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5d1e3pa1 A:263-345                                                                  d1e3pa4 A:346-482 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4                          d1e3pa7 A:483-578                                                                               d1e3pa5                   A:579-634                                          d1e3pa 2 A:656-7   17                                          SCOP domains
               CATH domains 1e3pA01 A:3-252 GHMP Kinase, N-terminal domain                                                                                                                                                                                                            ----------1e3pA02 A:263-345  [code=1.10.10.400, no name defined]                             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.hhh.eeeeeeee........eeeeeee...eeeeeeeee............eeeeeee.hhhhh.............hhhhhhhhhhhhhhhh..........eeeeeeeee......hhhhhhhhhhhhhhhh........eeeeeeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..............eeeee.......eeeeeee..eeeeeeeeeee.hhh.............eeeeee.hhhhhh........hhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee...hhhhhhhhhhhhhhhhhh.......eeeeeeeeeee....eeeeee...hhhhhhhh.eeeeeee....eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh................------------------..hhhhhhh..--------.....hhhhhh.---------------------......-.........---.....-------------------................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KH_TYPE_1  PDB: A:580-634 UniProt: 580-639                  -----------S1  PDB: A:656-717 UniProt: 651-723                                 PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3p A   3 NETHYAEAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYAAGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVVAINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDVAIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGEFPVFLDYQDDVLEALSAAVRPELSAALTIAGKQDREAELDRVKALAAEKLLPEFEGREKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGLISQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAALKQARDARLHILDVMMEAIDTPDEMSPNAPRIITV------------------NQIQEDTGAEI--------YIGAADGPAAEA---------------------GSVVKT-TFGAFVSLL---DGLLH-------------------LGVGQKVQVEIAEIDSRGK 717
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582  |      -         - |     612 |       -|      632 |       -         -   |    |-|       |-  |   |  -         -      |702       712     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                585                604       614      623        634                   656  661 |     671 675 679                 699                  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              663

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 1E3P)

Asymmetric Unit(hide GO term definitions)

Chain A (PNP_STRAT | Q53597)

molecular function
	GO:0000175	3'-5'-exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0004654	polyribonucleotide nucleotidyltransferase activity	Catalysis of the reaction: RNA(n+1) + phosphate <=> RNA(n) + a nucleoside diphosphate.
	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:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0006402	mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:154 - Pro A:155	[ RasMol ]
		Leu A:307 - Pro A:308	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	PNP_STRAT \| Q53597
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UniProtKB/Swiss-Prot
	PNP_STRAT \| Q53597	:	1e3h

1e3h	SEMET DERIVATIVE OF STREPTOMYCES ANTIBIOTICUS PNPASE/GPSI ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (5, 7)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File