1P4D - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   F FACTOR TRAI RELAXASE DOMAIN

Authors :   S. Datta, C. Larkin, J. F. Schildbach

Date :   22 Apr 03 (Deposition) - 14 Oct 03 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   5-Strand Antiparallel Beta Sheet, Alpha-Beta, 3 Histidine Mg(Ii) Coordination, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Datta, C. Larkin, J. F. Schildbach
Structural Insights Into Single-Stranded Dna Binding And Cleavage By F Factor Trai.
Structure V. 11 1369 2003
PubMed-ID: 14604527 | Reference-DOI: 10.1016/J.STR.2003.10.001
(for further references see the PDB file header)

Molecule 1 - TRAI PROTEIN
	Chains	:	A, B, C
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	36 KDA N-TERMINAL DOMAIN OF TRAI (RESIDUES 1-330)
	Gene	:	TRAI
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:146 , HIS A:157 , HIS A:159 , HOH A:942 , HOH A:956 , HOH A:981	BINDING SITE FOR RESIDUE MG A 900
02	AC2	SOFTWARE	HIS B:146 , HIS B:157 , HIS B:159 , HOH B:934	BINDING SITE FOR RESIDUE MG B 901
03	AC3	SOFTWARE	HIS C:146 , HIS C:157 , HIS C:159 , HOH C:905	BINDING SITE FOR RESIDUE MG C 902
04	AC4	SOFTWARE	ARG A:101 , GLN A:108 , GLN A:207 , ARG B:115 , EDO B:605	BINDING SITE FOR RESIDUE EDO A 600
05	AC5	SOFTWARE	LYS A:100 , ASP A:104	BINDING SITE FOR RESIDUE EDO A 601
06	AC6	SOFTWARE	ARG C:101 , ASP C:104 , ALA C:105 , GLN C:108 , GLN C:207 , LEU C:211	BINDING SITE FOR RESIDUE EDO C 603
07	AC7	SOFTWARE	SER B:46	BINDING SITE FOR RESIDUE EDO B 604
08	AC8	SOFTWARE	GLN A:207 , EDO A:600 , PHE B:112 , LYS B:203	BINDING SITE FOR RESIDUE EDO B 605
09	AC9	SOFTWARE	PHE A:112 , GLN A:116	BINDING SITE FOR RESIDUE EDO A 606
10	BC1	SOFTWARE	SER B:12	BINDING SITE FOR RESIDUE EDO B 607
11	BC2	SOFTWARE	LYS A:282	BINDING SITE FOR RESIDUE EDO A 608
12	BC3	SOFTWARE	ASP A:128 , VAL B:125 , GLU B:171 , LYS B:173 , HOH B:950 , HOH B:951	BINDING SITE FOR RESIDUE EDO B 610
13	BC4	SOFTWARE	ALA A:34 , ASP A:111 , VAL A:114 , ARG A:115 , HOH A:926 , HOH A:934 , HOH A:979	BINDING SITE FOR RESIDUE EDO A 612

(no "SS Bond" information available for 1P4D)

(no "Cis Peptide Bond" information available for 1P4D)

(no "SAP(SNP)/Variant" information available for 1P4D)

(no "PROSITE Motif" information available for 1P4D)

(no "Exon" information available for 1P4D)

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:275
 aligned with TRAI1_ECOLI | P14565 from UniProtKB/Swiss-Prot  Length:1756

    Alignment length:307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       
          TRAI1_ECOLI     1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPG 307
               SCOP domains d1p4da_ A: F factor TraI relaxase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh........eeehhhhhhh......hhhhhhhhhh...........ee..ee....eeeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.....eeeeeeee.....eeeeeeeeee..eee..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......ee....hhhhhh--------------------------------.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4d A   1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFS--------------------------------VDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPG 307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -         -         -       270       280       290       300       
                                                                                                                                                                                                                                                                    235                              268

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with TRAI1_ECOLI | P14565 from UniProtKB/Swiss-Prot  Length:1756

    Alignment length:307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       
          TRAI1_ECOLI     1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPG 307
               SCOP domains d1p4db_ B: F factor TraI relaxase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh.......eeehhhhhhh......hhhhhhhhhh.....................eeeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.....eeeeeeee.....eeeeeeeeee..eee..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee......ee....hhhhhh-------------------------------..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4d B   1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFS-------------------------------HVDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPG 307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -         -         -      |270       280       290       300       
                                                                                                                                                                                                                                                                    235                             267

Chain C from PDB  Type:PROTEIN  Length:276
 aligned with TRAI1_ECOLI | P14565 from UniProtKB/Swiss-Prot  Length:1756

    Alignment length:307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       
          TRAI1_ECOLI     1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPG 307
               SCOP domains d1p4dc_ C: F factor TraI relaxase                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----TrwC-1p4dC01 C:6-288                                                                                                                                                                                                                                                                       ------------------- Pfam domains (1)
           Pfam domains (2) -----TrwC-1p4dC02 C:6-288                                                                                                                                                                                                                                                                       ------------------- Pfam domains (2)
           Pfam domains (3) -----TrwC-1p4dC03 C:6-288                                                                                                                                                                                                                                                                       ------------------- Pfam domains (3)
         Sec.struct. author .ee.......hhhhhhhhh............eeehhhhhhh..........hhhhhh.ee...ee.............eeeeeee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeeee....eeeee.....eeeeeeee.....eeeeeeeeee..eee..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.hhhh.ee..........-------------------------------..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4d C   1 MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFS-------------------------------HVDPEIKMAEWMQTLKETGFDIRAYRDAADQRADLRTLTPG 307
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -         -         -      |270       280       290       300       
                                                                                                                                                                                                                                                                    235                             267

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) (23004)

Fold: Origin of replication-binding domain, RBD-like (33)

Superfamily: Origin of replication-binding domain, RBD-like (33)

Family: Relaxase domain (6)

Protein domain: F factor TraI relaxase (1)

Escherichia coli [TaxId: 562] (1)

1a	d1p4da_	A:
1b	d1p4db_	B:
1c	d1p4dc_	C:

(no "CATH Domain" information available for 1P4D)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: TrwC] (9)

Family: TrwC (9)

Escherichia coli (strain K12) (3)

1a	TrwC-1p4dC01	C:6-288
1b	TrwC-1p4dC02	C:6-288
1c	TrwC-1p4dC03	C:6-288

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (TRAI1_ECOLI | P14565)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003678	DNA helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
	GO:0003917	DNA topoisomerase type I activity	Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
	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: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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0032508	DNA duplex unwinding	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
	GO:0000746	conjugation	The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	1p4d
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	TRAI1_ECOLI \| P14565	:	2a0i 2l8b 2q7t 2q7u 3fld

(no "Related Entries Specified in the PDB File" available for 1P4D)

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