3O0N - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THERMOTOGA MARITIMA RIBONUCLEOTIDE REDUCTASE, NRDJ, IN COMPLEX WITH DTTP AND ADENOSYLCOBALAMIN

Authors :   K. -M. Larsson, D. T. Logan, P. Nordlund

Date :   19 Jul 10 (Deposition) - 28 Jul 10 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B

Keywords :   Oxidoreductase, 10 Alpha/Beta Barrel, Adenosylcobalamin Dependent, Ribonucleotide Reductase, Reduction Ribonucleotide 2'-Oh Position, Effector Dttp, Coenzyme B12 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Larsson, D. T. Logan, P. Nordlund
Structural Basis For Adenosylcobalamin Activation In Adocbl-Dependent Ribonucleotide Reductases.
Acs Chem. Biol. V. 5 933 2010
PubMed-ID: 20672854 | Reference-DOI: 10.1021/CB1000845

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE
	Chains	:	A, B
	EC Number	:	1.17.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NRDJ, TM_0118
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 8)

No.	Name	Count	Type	Full Name
1	5AD	1	Ligand/Ion	5'-DEOXYADENOSINE
2	B12	1	Ligand/Ion	COBALAMIN
3	CL	1	Ligand/Ion	CHLORIDE ION
4	CO	1	Ligand/Ion	COBALT (II) ION
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	TTP	2	Ligand/Ion	THYMIDINE-5'-TRIPHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:141 , SER A:142 , ILE A:143 , ARG A:171 , VAL A:177 , ALA A:178 , GLY A:179 , ALA A:184 , SER A:185 , PHE A:190 , HOH A:646 , HOH A:661 , HOH A:668 , HOH A:817 , HOH A:818 , HOH A:826 , MG A:1002 , LYS B:158 , VAL B:200 , VAL B:201 , LYS B:202	BINDING SITE FOR RESIDUE TTP A 1001
2	AC2	SOFTWARE	VAL A:607	BINDING SITE FOR RESIDUE CL A 1004
3	AC3	SOFTWARE	HOH A:665 , HOH A:668 , HOH A:817 , TTP A:1001	BINDING SITE FOR RESIDUE MG A 1002
4	AC4	SOFTWARE	HOH B:925 , HOH B:933 , HOH B:934 , HOH B:935 , TTP B:1001	BINDING SITE FOR RESIDUE MG B 1002
5	AC5	SOFTWARE	LYS A:158 , VAL A:200 , VAL A:201 , ASP B:141 , SER B:142 , ILE B:143 , ARG B:171 , VAL B:177 , ALA B:178 , GLY B:179 , ALA B:184 , SER B:185 , PHE B:190 , HOH B:679 , HOH B:731 , HOH B:925 , HOH B:934 , HOH B:946 , MG B:1002	BINDING SITE FOR RESIDUE TTP B 1001
6	AC6	SOFTWARE	ARG B:26 , ASN B:242 , GLY B:294 , ASP B:295 , CYS B:322 , GLY B:492 , SER B:502 , PHE B:508 , ARG B:514 , LYS B:547 , GLU B:551 , THR B:598 , ASN B:600 , THR B:626 , VAL B:627 , TYR B:628 , LEU B:633 , HOH B:674 , HOH B:756 , HOH B:953 , HOH B:954 , 5AD B:1004	BINDING SITE FOR RESIDUE B12 B 1003
7	AC7	SOFTWARE	MET B:212 , LEU B:243 , SER B:244 , CYS B:322 , GLY B:323 , SER B:596 , HOH B:735 , HOH B:760 , HOH B:937 , HOH B:942 , B12 B:1003	BINDING SITE FOR RESIDUE 5AD B 1004

(no "SS Bond" information available for 3O0N)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:295	-	Pro A:296
2	Tyr A:311	-	Pro A:312
3	Asp B:295	-	Pro B:296
4	Tyr B:311	-	Pro B:312

(no "SAP(SNP)/Variant" information available for 3O0N)

(no "PROSITE Motif" information available for 3O0N)

(no "Exon" information available for 3O0N)

Asymmetric/Biological 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:607
 aligned with O33839_THEMT | O33839 from UniProtKB/TrEMBL  Length:827

    Alignment length:633
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
         O33839_THEMT     1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGYRRRGALMGILNINHPDIEEFIDAKKENTGEAVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhh...........hhhhhhhhhhhhhhhh.........eee.....hhhhhhhhhhhhhhhhhh..eeeee...................hhhhhhhhhhhhhhh.--------.eeeeee....hhhhhhh...------....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhhh........eeee......eee...eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh............hhhhhhhhhhhh..............hhhhhhhh............ee.------------..ee..hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0n A   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVV--------ALMGILNINHPDIEEFIDAKK------VLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYT------------LLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510  |      -     | 530       540       550       560       570       580       590       600       610       620       630   
                                                                                                                                                                                                                                  201      210                 230    237                                                                                                                                                                                                                                                                                 513          526

Chain B from PDB  Type:PROTEIN  Length:611
 aligned with O33839_THEMT | O33839 from UniProtKB/TrEMBL  Length:827

    Alignment length:633
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
         O33839_THEMT     1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGYRRRGALMGILNINHPDIEEFIDAKKENTGEAVLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRFVTKEDGTKEPLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhh.........eee.....hhhhhhhhhhhhhhhhhhh.eeeee..........hhhhh....hhhhhhhhhhhhhhh..-------.eeeeee....hhhhhhh...------....eeeeee...hhhhhhhhhhh..eeeeee..eeeeeeeehhhhhhhhhhhhhhhh..eeehhhhhhhh........eeee......eee...eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhhhhh................hhhhhh............eeee.---------.eeee..hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh.........eee....hhhhhhhhhhhhhhh...ee.eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0n B   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVK-------ALMGILNINHPDIEEFIDAKK------VLNFFNLSVGFPMDKKEILKLYEEDGELELSHPRSTIRKKVKIRELFRKIATNAWKSGDPGLAFLGEMNKYYPLYPHRKINSTNPCGEIGLSDYEACNLGSIDVAKFYNNGFVDLEALQELVQIAVRFLDNVIDVNVFPIDKITKAVKESRRLGLGIMGFADLLYKLEIPYNSQEARDFAANLMAFIALHAHRTSYELGKEKGNFPLLEISRYRTEDNFVPFAMGMSNYDDEIREVMKMTKEFRRNVALLTIAPTGSISNIADTSSGLEPNFLLAYTRF---------PLLYVNQVLREKLNPEILKRIEKELIEKGSLKDIPDVPEKIKKVFVVALDIDPMDHLLMQDAFQRYVDNNISKTINMPQSATVDDVLNVYLEALRTNVRGITVYRDGSL 633
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510    |    -    |  530       540       550       560       570       580       590       600       610       620       630   
                                                                                                                                                                                                                                   202     210                 230    237                                                                                                                                                                                                                                                                                   515       525

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 "SCOP Domain" information available for 3O0N)

(no "CATH Domain" information available for 3O0N)

(no "Pfam Domain" information available for 3O0N)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O33839_THEMT | O33839)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0031419	cobalamin binding	Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	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.
	GO:0004748	ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor	Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		5AD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		B12	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC6	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Asp A:295 - Pro A:296	[ RasMol ]
		Asp B:295 - Pro B:296	[ RasMol ]
		Tyr A:311 - Pro A:312	[ RasMol ]
		Tyr B:311 - Pro B:312	[ RasMol ]

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	3o0n
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
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	O33839_THEMT \| O33839
		Comparative Protein Structure Models	:	ModBase
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	1.17.4.1
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/TrEMBL
	O33839_THEMT \| O33839	:	1xje 1xjf 1xjg 1xjj 1xjk 1xjm 1xjn 3o0o 3o0q

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (6, 6)

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