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(-) Description

Title :  THERMOTOGA MARITIMA RIBONUCLEOTIDE REDUCTASE, NRDJ, IN COMPLEX WITH DTTP, GDP 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 :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, 10 Alpha/Beta Barrel, Adenosylcobalamin Dependent, Ribonucleotide Reductase, Reduction Ribonucleotide 2'-Oh Position, Effector, Dttp, Substrate, Gdp, 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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2B122Ligand/IonCOBALAMIN
3GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
5TTP2Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:141 , SER A:142 , ILE A:143 , ILE A:146 , ARG A:171 , VAL A:177 , ALA A:178 , GLY A:179 , ALA A:184 , SER A:185 , PHE A:190 , HOH A:649 , HOH A:651 , HOH A:676 , HOH A:680 , HOH A:700 , HOH A:750 , HOH A:755 , MG A:1002 , LYS B:158 , VAL B:200 , VAL B:201 , LYS B:202BINDING SITE FOR RESIDUE TTP A 1001
02AC2SOFTWAREHOH A:649 , HOH A:679 , HOH A:749 , TTP A:1001BINDING SITE FOR RESIDUE MG A 1002
03AC3SOFTWAREASN A:90 , SER A:91 , PRO A:92 , PHE A:95 , ALA A:133 , CYS A:134 , GLY A:161 , GLY A:162 , ARG A:207 , ARG A:208 , ASN A:320 , PRO A:321 , CYS A:322 , GLU A:324 , ALA A:489 , PRO A:490 , THR A:491 , GLY A:492 , SER A:493 , ILE A:494 , HOH A:703 , HOH A:719 , B12 A:1004BINDING SITE FOR RESIDUE GDP A 1003
04AC4SOFTWAREARG A:208 , GLY A:294 , CYS A:322 , GLY A:492 , ASN A:496 , PHE A:508 , THR A:598 , ASN A:600 , THR A:626 , TYR A:628 , ASP A:630 , HOH A:693 , HOH A:726 , HOH A:780 , HOH A:782 , GDP A:1003 , 5AD A:1005BINDING SITE FOR RESIDUE B12 A 1004
05AC5SOFTWAREASN A:242 , LEU A:243 , SER A:244 , ASP A:295 , CYS A:322 , SER A:596 , THR A:598 , THR A:626 , HOH A:707 , HOH A:785 , B12 A:1004BINDING SITE FOR RESIDUE 5AD A 1005
06AC6SOFTWARELYS A:158 , VAL A:200 , LYS A:202 , 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:700 , HOH B:801 , MG B:1002BINDING SITE FOR RESIDUE TTP B 1001
07AC7SOFTWARESER B:142 , HOH B:801 , TTP B:1001BINDING SITE FOR RESIDUE MG B 1002
08AC8SOFTWAREASN B:90 , SER B:91 , PHE B:95 , ALA B:133 , CYS B:134 , GLY B:161 , ARG B:206 , ARG B:208 , ALA B:210 , ASN B:320 , PRO B:321 , CYS B:322 , GLU B:324 , ALA B:489 , PRO B:490 , THR B:491 , GLY B:492 , SER B:493 , ILE B:494 , HOH B:645 , HOH B:689 , HOH B:785 , HOH B:947 , HOH B:948 , B12 B:1004BINDING SITE FOR RESIDUE GDP B 1003
09AC9SOFTWAREARG B:26 , ARG B:206 , ARG B:208 , ASN B:242 , GLY B:294 , ASP B:295 , CYS B:322 , GLY B:492 , ASN B:496 , PHE B:508 , ASN B:600 , TYR B:628 , HOH B:705 , HOH B:714 , HOH B:726 , HOH B:736 , HOH B:812 , HOH B:879 , HOH B:947 , HOH B:950 , HOH B:955 , GDP B:1003 , 5AD B:1005BINDING SITE FOR RESIDUE B12 B 1004
10BC1SOFTWAREMET B:212 , ASN B:242 , LEU B:243 , SER B:244 , CYS B:322 , GLY B:323 , SER B:596 , THR B:626 , HOH B:682 , HOH B:758 , HOH B:798 , HOH B:880 , B12 B:1004BINDING SITE FOR RESIDUE 5AD B 1005

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:134 -B:333

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp A:295 -Pro A:296
2Tyr A:311 -Pro A:312
3Gln B:203 -Gly B:204
4Gly B:204 -Ser B:205
5Asp B:295 -Pro B:296
6Tyr B:311 -Pro B:312

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O0O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O0O)

(-) Exons   (0, 0)

(no "Exon" information available for 3O0O)

(-) Sequences/Alignments

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:612
 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..-----hhhhhhhhhhhhhhhhhh..eeehhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhh.........eee.....hhhhhhhhhhhhhhhhhhh.eeeee.........ee....ee..hhhhhhhhhhhhhhh.....-....eeeeee....hhhhhhh...------....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhhh..........ee......ee....eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............hhhhhhhhhhhh..............hhhhhhhh............eeee.---------.eeeehhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0o A   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPS-----KLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGS-RRGALMGILNINHPDIEEFIDAKK------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   
                                                                                       61    67                                                                                                                                       205 |                    230    237                                                                                                                                                                                                                                                                                   515       525                                                                                                            
                                                                                                                                                                                                                                        207                                                                                                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:618
 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..................hhhhhhhhhhhhhhh...........eeeeee....hhhhhhh...------....eeeeee...hhhhhhhhhhh..eeee........eeeehhhhhhhhhhhhhhhh..eeehhhhhhhh..........ee......ee....eeeeeeee....ee..eehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh............hhhhhhhhhhhh..............hhhhhhhh............eeee.---------.eeeehhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.hhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o0o B   1 MKLSDLISRWIDVEPSKNAQIILRDRYFMKDLDGNYLETKWEDVARRVARVVATAELLNPSYKKNEKLDRIKEWEDIFFRVLKARLFIPNSPTLFNAGLGVKHDLLWKPIDQMTLEDYEEIYRSRNHLHMLSACFVVPVGDSIEEIFEAVKEYALITKVGGGVGSNFSELRPKGSFVAGTHGKASGPVSFMHVFNSAISVVKQGSRRRGALMGILNINHPDIEEFIDAKK------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   
                                                                                                                                                                                                                                                               230    237                                                                                                                                                                                                                                                                                   515       525
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3O0O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O0O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O0O)

(-) Gene Ontology  (6, 6)

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.

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  3o0o
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  O33839_THEMT | O33839
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  1.17.4.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        O33839_THEMT | O33839: 1xje 1xjf 1xjg 1xjj 1xjk 1xjm 1xjn 3o0n 3o0q

(-) Related Entries Specified in the PDB File

1xje 1xjf 1xjg 1xjj 1xjm 1xjn 3o0n 3o0q