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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE CLASS I RIBONUCLEOTIDE REDUCTASE (NP_241368.1) FROM BACILLUS HALODURANS AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  19 Sep 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  A,B,C  (2x)
Keywords :  Np_241368. 1, Putative Class I Ribonucleotide Reductase, Ribonucleotide Reductase, Small Chain, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Dna Replication, Iron, Metal-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Class I Ribonucleotide Reductase (Np_241368. 1) From Bacillus Halodurans At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT BETA
    Atcc: BAA-125
    Chains: A, B, C
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_241368.1, NRDB, BH0502
    Organism Scientific: BACILLUS HALODURANS C-125
    Organism Taxid: 272558
    Strain: C-125, DSM 18197, FERM 7344, JCM 9153
    Synonym: RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C
Biological Unit 3 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 47)

Asymmetric Unit (7, 47)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL3Ligand/IonGLYCEROL
3MSE31Mod. Amino AcidSELENOMETHIONINE
4PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7ZN4Ligand/IonZINC ION
Biological Unit 1 (6, 29)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MSE21Mod. Amino AcidSELENOMETHIONINE
4PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 28)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2GOL2Ligand/IonGLYCEROL
3MSE20Mod. Amino AcidSELENOMETHIONINE
4PEG6Ligand/IonDI(HYDROXYETHYL)ETHER
5PG4-1Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION
Biological Unit 3 (6, 86)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL6Ligand/IonGLYCEROL
3MSE62Mod. Amino AcidSELENOMETHIONINE
4PEG12Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE2Ligand/IonTRIETHYLENE GLYCOL
7ZN-1Ligand/IonZINC ION

(-) Sites  (0, 0)

(no "Site" information available for 2RCC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RCC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RCC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RCC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RCC)

(-) Exons   (0, 0)

(no "Exon" information available for 2RCC)

(-) Sequences/Alignments

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:313
 aligned with RIR2_BACHD | Q9KFH7 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:313
                             1                                                                                                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309   
           RIR2_BACHD     - -MEQLQKRKIYDTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSMRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWI 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------2rccA01 A:38-296 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                               ---------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rcc A   0 GmEQLQKRKIYDTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNmLANFWTPFEINmSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSmRAAEYLTDSSLAALmSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKmVSTSTmINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLmKAADLEKDWFRYIIGDKIPGINPEDmETYISFIANKRAVQLGmEKPYPEIKHNPmKWI 312
                             |       9        19        29        39       |49        59        69        79        89      | 99       109 |     119       129       139       149       159       169       179       189       199     | 209 |     219       229       239       249    |  259       269       279|      289       299       309   
                             |                                            47-MSE      59-MSE                               96-MSE        111-MSE                                                                                       205-MSE |                                        254-MSE                   280-MSE          297-MSE     309-MSE
                             1-MSE                                                                                                                                                                                                           211-MSE                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with RIR2_BACHD | Q9KFH7 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:280
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316
           RIR2_BACHD    37 FSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSMRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWIRAYE 316
               SCOP domains d2rccb_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -2rccB01 B:38-296 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                               -------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rcc B  37 FSWAYPLYKNmLANFWTPFEINmSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSmRAAEYLTDSSLAALmSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKmVSTSTmINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLmKAADLEKDWFRYIIGDKIPGINPEDmETYISFIANKRAVQLGmEKPYPEIKHNPmKWIRAYE 316
                                    46|       56  |     66        76        86        96       106    |  116       126       136       146       156       166       176       186       196       206    |  216       226       236       246       256       266       276   |   286       296|      306  |    316
                                     47-MSE      59-MSE                               96-MSE        111-MSE                                                                                       205-MSE |                                        254-MSE                   280-MSE          297-MSE     309-MSE   
                                                                                                                                                                                                        211-MSE                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:311
 aligned with RIR2_BACHD | Q9KFH7 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
           RIR2_BACHD     3 QLQKRKIYDTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNMLANFWTPFEINMSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSMRAAEYLTDSSLAALMSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKMVSTSTMINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLMKAADLEKDWFRYIIGDKIPGINPEDMETYISFIANKRAVQLGMEKPYPEIKHNPMKWIR 313
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------2rccC01 C:38-296 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                               ----------------- CATH domains
           Pfam domains (1) -------------------------Ribonuc_red_sm-2rccC01 C:28-310                                                                                                                                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) -------------------------Ribonuc_red_sm-2rccC02 C:28-310                                                                                                                                                                                                                                                            --- Pfam domains (2)
           Pfam domains (3) -------------------------Ribonuc_red_sm-2rccC03 C:28-310                                                                                                                                                                                                                                                            --- Pfam domains (3)
         Sec.struct. author ....................................hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rcc C   3 QLQKRKIYDTTASNASTGILNGKSSNVLNWDDVRFSWAYPLYKNmLANFWTPFEINmSHDAKQFPTLTETEQEAFKKIIGLLAFLDSVQTDYSmRAAEYLTDSSLAALmSVLSFQEVVHNQSYSYVLSSLVPKATQDEIFEYWKHDDVLKERNEFIIDGYEKFVDNPTPKTFLESIVYDVILEGLNFYSGFAFFYNLARNQKmVSTSTmINYINRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLmKAADLEKDWFRYIIGDKIPGINPEDmETYISFIANKRAVQLGmEKPYPEIKHNPmKWIR 313
                                    12        22        32        42    |   52      | 62        72        82        92   |   102       112       122       132       142       152       162       172       182       192       202  |    212       222       232       242       252 |     262       272       282       292    |  302      |312 
                                                                       47-MSE      59-MSE                               96-MSE        111-MSE                                                                                       205-MSE |                                        254-MSE                   280-MSE          297-MSE     309-MSE
                                                                                                                                                                                                                                          211-MSE
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RIR2_BACHD | Q9KFH7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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:0009186    deoxyribonucleoside diphosphate metabolic process    The chemical reactions and pathways involving a deoxyribonucleoside diphosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with diphosphate on the sugar.
    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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