1NPP - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NUSG IN P2(1)

Authors :   J. R. Knowlton, M. Bubunenko, M. Andrykovitch, W. Guo, K. M. Routzahn, D. S. Waugh, D. L. Court, X. Ji

Date :   18 Jan 03 (Deposition) - 11 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: A,B  (1x)

Keywords :   Rnap Transcription Factor, Nusg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Knowlton, M. Bubunenko, M. Andrykovitch, W. Guo, K. M. Routzahn, D. S. Waugh, D. L. Court, X. Ji
A Spring-Loaded State Of Nusg In Its Functional Cycle Is Suggested By X-Ray Crystallography And Supported By Site-Directed Mutants
Biochemistry V. 42 2275 2003
PubMed-ID: 12600194 | Reference-DOI: 10.1021/BI0272508
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PKM702
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NUSG OR AQ_1931
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	IPA	-1	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	IPA	-1	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	IPA	-1	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	IPA	2	Ligand/Ion	ISOPROPYL ALCOHOL

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	IPA	-1	Ligand/Ion	ISOPROPYL ALCOHOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH D:1063	BINDING SITE FOR RESIDUE IPA D 859
2	AC2	SOFTWARE	GLU D:37 , MET D:151 , LYS D:155 , HOH D:1055 , HOH D:1073	BINDING SITE FOR RESIDUE IPA D 860

Asymmetric Unit

No.	Residues
1	A:104	-	A:119
2	B:104	-	B:119
3	C:104	-	C:119
4	D:104	-	D:119

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUSG	PS01014	Transcription termination factor nusG signature.	NUSG_AQUAE	231-240	4	A:231-240 B:231-240 C:231-240 D:231-240

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUSG	PS01014	Transcription termination factor nusG signature.	NUSG_AQUAE	231-240	1	A:231-240 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUSG	PS01014	Transcription termination factor nusG signature.	NUSG_AQUAE	231-240	1	- B:231-240 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUSG	PS01014	Transcription termination factor nusG signature.	NUSG_AQUAE	231-240	1	- - C:231-240 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUSG	PS01014	Transcription termination factor nusG signature.	NUSG_AQUAE	231-240	1	- - - D:231-240

Biological Unit 5 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUSG	PS01014	Transcription termination factor nusG signature.	NUSG_AQUAE	231-240	2	A:231-240 B:231-240 - -

(no "Exon" information available for 1NPP)

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:244
 aligned with NUSG_AQUAE | O67757 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:244
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244    
           NUSG_AQUAE     5 QVQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI 248
               SCOP domains d1nppa3 A:5-50,A:132-190                      d1nppa1 A:51-131 N-utilization substance G protein NusG, insert domain           d1nppa3 A:5-50,A:132-190                                   d1nppa2 A:191-248                                          SCOP domains
               CATH domains ----1nppA01 A:9-49,A:132-185                 1nppA02 A:50-131 NusG, domain 2                                                   1nppA01 A:9-49,A:132-185                              1nppA03 A:186-247  [code=2.30.30.30, no name defined]         - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeee...hhhhhhhhhhhhhhhh.hhh.eeeee....eeeeeee...eeeeee.....eeeeee....eeeeeee..eeeeee....hhhhhh........eeee....eeeeeee.......eeeeee..hhhhhhhhhh...eeee.ee..ee...hhhhhhhhhhhhhhh............eeee........eeeeeeee....eeeeeeee..eeeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NUSG      -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npp A   5 QVQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI 248
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with NUSG_AQUAE | O67757 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:241
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247 
           NUSG_AQUAE     8 ELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI 248
               SCOP domains d1nppb3 B:8-50,B:132-190                   d1nppb1 B:51-131 N-utilization substance G protein NusG, insert domain           d1nppb3 B:8-50,B:132-190                                   d1nppb2 B:191-248                                          SCOP domains
               CATH domains -1nppB01 B:9-49,B:132-185                 1nppB02 B:50-131 NusG, domain 2                                                   1nppB01 B:9-49,B:132-185                              1nppB03 B:186-248  [code=2.30.30.30, no name defined]           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhhhhhhhhhhhhh.hhh.eeeee...eeeeeeee..eeeeeee.....eeeeee....eeeeeee..eeeeee....hhhhhh........eeee....eeeeeeee......eeeeee..hhhhhhhhhh...eeee.ee..ee...hhhhhhhhhhhhhhh............eeee........eeeeee......eeeeeeee..eeeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NUSG      -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npp B   8 ELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEKI 248
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain C from PDB  Type:PROTEIN  Length:238
 aligned with NUSG_AQUAE | O67757 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:238
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239        
           NUSG_AQUAE    10 EKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEK 247
               SCOP domains d1nppc3 C:10-50,C:132-190                d1nppc1 C:51-131 N-utilization substance G protein NusG, insert domain           d1nppc3 C:10-50,C:132-190                                  d1nppc2 C:191-247                                         SCOP domains
               CATH domains 1nppC01 C:10-49,C:132-185               1nppC02 C:50-131 NusG, domain 2                                                   1nppC01 C:10-49,C:132-185                             1nppC03 C:186-246  [code=2.30.30.30, no name defined]        - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhhhhhhhhhh.eeeee...eeeeeeee..eeeeeee.....eeeeee....eeeeeee..eeeeee....hhhhhh........eeee....eeeeeeee......eeeeee..hhhhhhhhhhh..eeee.ee..ee...hhhhhhhhhhhhhhh............eeee........eeeeeee......eeeeeee..eeeeee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NUSG      ------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1npp C  10 EKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQVEK 247
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239

Chain D from PDB  Type:PROTEIN  Length:240
 aligned with NUSG_AQUAE | O67757 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:240
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245
           NUSG_AQUAE     6 VQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQV 245
               SCOP domains d1nppd3 D:6-50,D:132-190                     d1nppd1 D:51-131 N-utilization substance G protein NusG, insert domain           d1nppd3 D:6-50,D:132-190                                   d1nppd2 D:191-245                                       SCOP domains
               CATH domains ---1nppD01 D:9-49,D:132-185                 1nppD02 D:50-131 NusG, domain 2                                                   1nppD01 D:9-49,D:132-185                              1nppD03 D:186-245  [code=2.30.30.30, no name defined]        CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------NusG-1nppD05 D:81-175                                                                          ---------------------KOW-1nppD01 D:197-232               ------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------NusG-1nppD06 D:81-175                                                                          ---------------------KOW-1nppD02 D:197-232               ------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------NusG-1nppD07 D:81-175                                                                          ---------------------KOW-1nppD03 D:197-232               ------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------NusG-1nppD08 D:81-175                                                                          ---------------------KOW-1nppD04 D:197-232               ------------- Pfam domains (4)
         Sec.struct. author ......eeeeeee...hhhhhhhhhhhhhhhh.hhh.eeeee...eeeeeeee..eeeeeee.....eeeeee....eeeeeee..eeeeee.....hhhhh........eeee....eeeeeeee......eeeeee..hhhhhhhhhh...eeee.ee..ee.eehhhhhhhhhhh................eee.........eeee.........eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NUSG      ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1npp D   6 VQELEKKWYALQVEPGKENEAKENLLKVLELEGLKDLVDEVIVPAEEKVVIRAQGKEKYRLSLKGNARDISVLGKKGVTTFRIENGEVKVVESVEGDTCVNAPPISKPGQKITCKENKTEAKIVLDNKIFPGYILIKAHMNDKLLMAIEKTPHVFRPVMVGGKPVPLKEEEVQNILNQIKRGVKPSKVEFEKGDQVRVIEGPFMNFTGTVEEVHPEKRKLTVMISIFGRMTPVELDFDQV 245
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.940, no name defined] (5)

Aquifex aeolicus. Organism_taxid: 63363. (2)

1a	1nppA01	A:9-49,A:132-185
1b	1nppB01	B:9-49,B:132-185
1c	1nppD01	D:9-49,D:132-185
1d	1nppC01	C:10-49,C:132-185

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.30, no name defined] (111)

Aquifex aeolicus. Organism_taxid: 63363. (2)

2a	1nppB03	B:186-248
2b	1nppA03	A:186-247
2c	1nppC03	C:186-246
2d	1nppD03	D:186-245

Architecture: Sandwich (5577)

Topology: mini-chromosome maintenance (MCM) complex, domain 2 (4)

Homologous Superfamily: NusG, domain 2 (4)

Aquifex aeolicus. Organism_taxid: 63363. (2)

3a	1nppA02	A:50-131
3b	1nppB02	B:50-131
3c	1nppC02	C:50-131
3d	1nppD02	D:50-131

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: KOW (56)

Family: KOW (52)

Aquifex aeolicus (2)

1a	KOW-1nppD01	D:197-232
1b	KOW-1nppD02	D:197-232
1c	KOW-1nppD03	D:197-232
1d	KOW-1nppD04	D:197-232

Clan: NusG-like (8)

Family: NusG (8)

Aquifex aeolicus (3)

2a	NusG-1nppD05	D:81-175
2b	NusG-1nppD06	D:81-175
2c	NusG-1nppD07	D:81-175
2d	NusG-1nppD08	D:81-175

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NUSG_AQUAE | O67757)

biological process
	GO:0006354	DNA-templated transcription, elongation	The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
	GO:0006353	DNA-templated transcription, termination	The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
	GO:0032784	regulation of DNA-templated transcription, elongation	Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0031564	transcription antitermination	Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	1npp
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	NUSG_AQUAE \| O67757	:	1m1g 1m1h 1npr

1m1g	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS N-UTILIZATION SUBSTANCE G (NUSG), SPACE GROUP P2(1)
1m1h	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS N-UTILIZATION SUBSTANCE G (NUSG), SPACE GROUP I222
1npr

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (4, 4)

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