1M5R | PD0334 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   TERNARY COMPLEX OF T4 PHAGE BGT WITH UDP AND A 13 MER DNA DUPLEX

Authors :   L. Lariviere, S. Morera

Date :   10 Jul 02 (Deposition) - 11 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Protein-Dna Complex, Base-Flipping, Abasic Site, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Lariviere, S. Morera
A Base-Flipping Mechanism For The T4 Phage Beta-Glucosyltransferase And Identification Of A Transition State Analog
J. Mol. Biol. V. 324 483 2002
PubMed-ID: 12445783 | Reference-DOI: 10.1016/S0022-2836(02)01091-4
(for further references see the PDB file header)

*Molecule 1 - 5'-D(GPAPTPAPCPTP3DRPAPGPAPTPAPG)- 3'**
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(CPTPAPTPCPTPGPAPGPTPAPTPC)-3'**
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DNA BETA-GLUCOSYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.4.1.27
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PBSK
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BGT
	Organism Scientific	:	ENTEROBACTERIA PHAGE T4
	Organism Taxid	:	10665
	Synonym	:	BGT

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A		C		E
Biological Unit 2 (1x)	:		B		D		F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 12)

No.	Name	Count	Type	Full Name
1	3DR	2	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	5	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	3DR	1	Mod. Nucleotide	1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	TRS	3	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:18 , GLY A:188 , SER A:189 , ARG A:191 , ARG A:195 , PHE A:213 , GLY A:214 , LYS A:237 , ILE A:238 , MET A:240 , VAL A:243 , TYR A:261 , ARG A:269 , GLU A:272 , TRS A:500 , HOH A:1009 , HOH A:1019 , HOH A:1021 , HOH A:1023 , HOH A:1074 , HOH A:1089	BINDING SITE FOR RESIDUE UDP A 400
02	AC2	SOFTWARE	GLU A:22 , THR A:99 , ASP A:100 , ARG A:191 , UDP A:400 , HOH A:1008 , HOH A:1021 , HOH A:1172 , HOH A:1199	BINDING SITE FOR RESIDUE TRS A 500
03	AC3	SOFTWARE	VAL B:18 , GLY B:188 , SER B:189 , ARG B:191 , ARG B:195 , PHE B:213 , GLY B:214 , LYS B:237 , ILE B:238 , MET B:240 , VAL B:243 , TYR B:261 , LEU B:268 , ARG B:269 , GLU B:272 , TRS B:501 , HOH B:2001 , HOH B:2002 , HOH B:2003 , HOH B:2004 , HOH B:2038 , HOH B:2081	BINDING SITE FOR RESIDUE UDP B 401
04	AC4	SOFTWARE	GLU B:22 , THR B:99 , ASP B:100 , UDP B:401 , HOH B:2004 , HOH B:2036 , HOH B:2115 , HOH B:2217	BINDING SITE FOR RESIDUE TRS B 501
05	AC5	SOFTWARE	GLU A:340 , TRP A:341 , ALA A:344 , HOH A:1121 , HOH A:1122 , HOH A:1260 , HOH A:1380	BINDING SITE FOR RESIDUE TRS A 501
06	AC6	SOFTWARE	ASN B:57 , TYR B:59 , TYR B:90 , LYS B:91 , SER B:92 , HOH B:2012 , HOH B:2026 , HOH B:2195	BINDING SITE FOR RESIDUE TRS B 502
07	AC7	SOFTWARE	MET B:242 , GLN B:249	BINDING SITE FOR RESIDUE TRS B 503
08	AC8	SOFTWARE	ARG A:291 , THR A:334 , HOH A:1078 , HOH A:1127 , HOH A:1252	BINDING SITE FOR RESIDUE MPD A 502
09	AC9	SOFTWARE	LYS B:180 , LEU B:182 , ASP B:183 , ASN B:209	BINDING SITE FOR RESIDUE MPD B 504
10	BC1	SOFTWARE	GLY A:45 , VAL A:46 , TYR B:159 , ARG B:291 , HOH B:2205 , HOH B:2288 , HOH B:2301 , HOH B:2378	BINDING SITE FOR RESIDUE MPD B 505

(no "SS Bond" information available for 1M5R)

(no "Cis Peptide Bond" information available for 1M5R)

(no "SAP(SNP)/Variant" information available for 1M5R)

(no "PROSITE Motif" information available for 1M5R)

(no "Exon" information available for 1M5R)

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:351
 aligned with GSTB_BPT4 | P04547 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    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       310       320       330       340       350 
            GSTB_BPT4     1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
               SCOP domains d1m5ra_ A: beta-Glucosyltransferase (DNA-modifying)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m5rA01 A:1-166,A:333-349 Glycogen Phosphorylase B;                                                                                                                   1m5rA02 A:167-332 Glycogen Phosphorylase B;                                                                                                                           1m5rA01          -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhhhhhhhhhh...eeeeee......eee.hhhhhhhh.eeeee.....hhhhh.hhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhh.....eeeeee.hhhhhhhhh............eeeeee..hhhhhhhhhhhhhhh.....eeee...hhhhh...........eee...hhhhhhhhhh.eeeeee..hhhhh....hhhhhhhhh...eeeee.hhhh......hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m5r A   1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
                                    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       310       320       330       340       350

Chain B from PDB  Type:PROTEIN  Length:351
 aligned with GSTB_BPT4 | P04547 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    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       310       320       330       340       350 
            GSTB_BPT4     1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
               SCOP domains d1m5rb_ B: beta-Glucosyltransferase (DNA-modifying)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m5rB01 B:1-166,B:333-349 Glycogen Phosphorylase B;                                                                                                                   1m5rB02 B:167-332 Glycogen Phosphorylase B;                                                                                                                           1m5rB01          -- CATH domains
           Pfam domains (1) T4-Gluco-transf-1m5rB01 B:1-38        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) T4-Gluco-transf-1m5rB02 B:1-38        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.........hhhhhhhhhhhhhhhh...eeeeee......eee.hhhhhhhh.eeeee.....hhhhh.hhhhhhhhhhhhhh...eeeee.........hhhhhh...hhhhhhhhhhh....eeeee...hhhhhhhhh.....eeeeee.hhhhhhhhh............eeeeee..hhhhhhhhhhhhhhh.....eeee...hhhhh...........eee...hhhhhhhhhh.eeeeee..hhhhh....hhhhhhhhh...eeeee.hhh.......hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m5r B   1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
                                    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       310       320       330       340       350

Chain C from PDB  Type:DNA  Length:13
                                             
                 1m5r C   1 GATACTxAGATAG  13
                                  | 10   
                                  7-3DR

Chain D from PDB  Type:DNA  Length:13
                                             
                 1m5r D   1 GATACTxAGATAG  13
                                  | 10   
                                  7-3DR

Chain E from PDB  Type:DNA  Length:13
                                             
                 1m5r E  14 CTATCTGAGTATC  26
                                    23

Chain F from PDB  Type:DNA  Length:13
                                             
                 1m5r F  14 CTATCTGAGTATC  26
                                    23

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: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Glycogen Phosphorylase B; (202)

[unclassified] (4)

1a	1m5rA01	A:1-166,A:333-349
1b	1m5rB01	B:1-166,B:333-349
1c	1m5rA02	A:167-332
1d	1m5rB02	B:167-332

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: T4-Gluco-transf] (12)

Family: T4-Gluco-transf (12)

Enterobacteria phage T4 (Bacteriophage T4) (12)

1a	T4-Gluco-transf-1m5rB01	B:1-38
1b	T4-Gluco-transf-1m5rB02	B:1-38

Asymmetric Unit(hide GO term definitions)

Chain A,B (GSTB_BPT4 | P04547)

molecular function
	GO:0033821	DNA beta-glucosyltransferase activity	Catalysis of the transfer of a beta-D-glucosyl residue from UDP-glucose to a hydroxymethylcytosine residue in DNA.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006304	DNA modification	The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

Asymmetric Unit
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	Cis Peptide Bonds
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Biological Units
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	1m5r
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1ixy	1IXY CONTAINS THE SAME STRUCTRUE WITH MAGNESIUM ION BOUND TO THE ACTIVE SITE
1jg6	T4 PHAGE BGT IN COMPLEX WITH UDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 4)

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