3NBF - JenaLib

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Title :   Q28E MUTANT OF HERA HELICASE N-TERMINAL DOMAIN BOUND TO 8-OXO-ADP

Authors :   M. G. Rudolph, D. Klostermeier

Date :   03 Jun 10 (Deposition) - 23 Mar 11 (Release) - 23 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Rna Helicase, Ribosome Biogenesis, Atp Hydrolysis, Base Specificity, Thermostability, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Strohmeier, I. Hertel, U. Diederichsen, M. G. Rudolph, D. Klostermeier
Changing Nucleotide Specificity Of The Dead-Box Helicase Hera Abrogates Communication Between The Q-Motif And The P-Loop.
Biol. Chem. V. 392 357 2011
PubMed-ID: 21391900 | Reference-DOI: 10.1515/BC.2011.034

Molecule 1 - HEAT RESISTANT RNA DEPENDENT ATPASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Fragment	:	N-TERMINAL DOMAIN
	Mutation	:	YES
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	262724
	Strain	:	HB27

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	8OD	6	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL PHOSPHONO HYDROGENPHOSPHATE
2	8OP	3	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	8OD	4	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL PHOSPHONO HYDROGENPHOSPHATE
2	8OP	-1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	8OD	2	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL PHOSPHONO HYDROGENPHOSPHATE
2	8OP	3	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:3 , LEU A:21 , THR A:23 , PRO A:24 , GLU A:28 , THR A:49 , GLY A:50 , LYS A:51 , THR A:52 , GLU A:91 , HOH A:212 , HOH A:272 , HOH A:282 , THR B:108 , GLY B:109 , LYS B:112 , ARG C:191	BINDING SITE FOR RESIDUE 8OD A 500
2	AC2	SOFTWARE	PRO A:80 , THR A:81 , ARG A:82 , GLU A:83 , GLY A:106 , THR A:127 , GLY A:129 , ARG A:130 , PHE A:161 , HOH A:235 , 8OD B:600	BINDING SITE FOR RESIDUE 8OD A 600
3	AC3	SOFTWARE	THR A:108 , LEU B:21 , THR B:23 , PRO B:24 , THR B:25 , GLU B:28 , THR B:47 , GLY B:48 , THR B:49 , GLY B:50 , LYS B:51 , THR B:52 , GLU B:91 , HOH B:228 , HOH B:237 , HOH B:248 , HOH B:249	BINDING SITE FOR RESIDUE 8OD B 500
4	AC4	SOFTWARE	ARG A:82 , 8OD A:600 , THR B:81 , ARG B:82 , GLU B:83 , GLY B:106 , THR B:127 , GLY B:129 , ARG B:130 , PHE B:161 , HOH B:226	BINDING SITE FOR RESIDUE 8OD B 600
5	AC5	SOFTWARE	LYS A:190 , GLU A:194 , GLN B:44 , ASN B:204 , ILE B:206 , HOH B:208 , TYR C:110 , GLY C:111 , LYS C:114 , GLN C:137 , HOH C:211 , HOH C:226 , HOH C:230 , HOH C:244 , HOH C:277	BINDING SITE FOR RESIDUE 8OP C 501
6	AC6	SOFTWARE	LEU C:21 , THR C:23 , THR C:25 , GLU C:28 , GLY C:48 , THR C:49 , GLY C:50 , LYS C:51 , THR C:52 , LEU C:53 , GLU C:91 , LYS D:112	BINDING SITE FOR RESIDUE 8OP C 500
7	AC7	SOFTWARE	ARG A:195 , HOH A:226 , PRO C:80 , THR C:81 , ARG C:82 , GLU C:83 , GLY C:106 , THR C:127 , GLY C:129 , ARG C:130 , MET C:159 , PHE C:161 , HOH C:210 , HOH C:214 , HOH C:254 , HOH C:255 , ARG D:82 , 8OD D:600	BINDING SITE FOR RESIDUE 8OD C 600
8	AC8	SOFTWARE	PHE D:3 , LEU D:21 , THR D:23 , PRO D:24 , THR D:25 , GLU D:28 , GLY D:50 , LYS D:51 , THR D:52 , GLU D:91	BINDING SITE FOR RESIDUE 8OP D 500
9	AC9	SOFTWARE	ARG C:82 , 8OD C:600 , THR D:81 , ARG D:82 , GLU D:83 , GLY D:106 , THR D:127 , GLY D:129 , ARG D:130 , MET D:159 , PHE D:161 , HOH D:217 , HOH D:240 , HOH D:245 , HOH D:248	BINDING SITE FOR RESIDUE 8OD D 600

(no "SS Bond" information available for 3NBF)

(no "Cis Peptide Bond" information available for 3NBF)

(no "SAP(SNP)/Variant" information available for 3NBF)

(no "PROSITE Motif" information available for 3NBF)

(no "Exon" information available for 3NBF)

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:207
 aligned with Q72GF3_THET2 | Q72GF3 from UniProtKB/TrEMBL  Length:517

    Alignment length:207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       
         Q72GF3_THET2     8 MEFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 214
               SCOP domains d3nbfa_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nbf A   1 MEFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain B from PDB  Type:PROTEIN  Length:206
 aligned with Q72GF3_THET2 | Q72GF3 from UniProtKB/TrEMBL  Length:517

    Alignment length:206
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208      
         Q72GF3_THET2     9 EFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 214
               SCOP domains d3nbfb_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nbf B   2 EFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with Q72GF3_THET2 | Q72GF3 from UniProtKB/TrEMBL  Length:517

    Alignment length:207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       
         Q72GF3_THET2     8 MEFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 214
               SCOP domains d3nbfc_ C: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhh......hhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhh.....eeeee....hhhhhhhhhhh....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nbf C   1 MEFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVIK 207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:202
 aligned with Q72GF3_THET2 | Q72GF3 from UniProtKB/TrEMBL  Length:517

    Alignment length:206
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
         Q72GF3_THET2     8 MEFKDFPLKPEILEALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI 213
               SCOP domains d3nbfd_ D: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------DEAD-3nbfD01 D:25-192                                                                                                                                                   -------------- Pfam domains (1)
           Pfam domains (2) ------------------------DEAD-3nbfD02 D:25-192                                                                                                                                                   -------------- Pfam domains (2)
           Pfam domains (3) ------------------------DEAD-3nbfD03 D:25-192                                                                                                                                                   -------------- Pfam domains (3)
           Pfam domains (4) ------------------------DEAD-3nbfD04 D:25-192                                                                                                                                                   -------------- Pfam domains (4)
         Sec.struct. author .hhhhh..hhhhhhhhhh......hhhhhhhhhhhhh...eeee.----..hhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh..eeeehhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nbf D   1 MEFKDFPLKPEILEALHGRGLTTPTPIEAAALPLALEGKDLIGQA----GKTLAFALPIAERLAPSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI 206
                                    10        20        30        40    |   50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
                                                                       45   50

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: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: automated matches (303)

Protein domain: automated matches (303)

Thermus thermophilus [TaxId: 262724] (12)

1a	d3nbfa_	A:
1b	d3nbfb_	B:
1c	d3nbfc_	C:
1d	d3nbfd_	D:

(no "CATH Domain" information available for 3NBF)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DEAD (41)

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (5)

1a	DEAD-3nbfD01	D:25-192
1b	DEAD-3nbfD02	D:25-192
1c	DEAD-3nbfD03	D:25-192
1d	DEAD-3nbfD04	D:25-192

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q72GF3_THET2 | Q72GF3)


GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nbf)

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Description

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Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

SS Bonds (0, 0)

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