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(-) Description

Title :  R2F FROM CORYNEBACTERIUM AMMONIAGENES IN ITS MN SUBSTITUTED FORM
 
Authors :  M. Hogbom, Y. Huque, B. M. Sjoberg, P. Nordlund
Date :  28 Nov 01  (Deposition) - 21 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix Bundle, Arm Exchange, Radical Protein, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hogbom, Y. Huque, B. M. Sjoberg, P. Nordlund
Crystal Structure Of The Di-Iron/Radical Protein Of Ribonucleotide Reductase From Corynebacterium Ammoniagenes.
Biochemistry V. 41 1381 2002
PubMed-ID: 11802741  |  Reference-DOI: 10.1021/BI011429L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOTIDE REDUCTASE PROTEIN R2F
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PIG056
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: CORYNEBACTERIUM AMMONIAGENES
    Organism Taxid: 1697

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MN10Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:77 , GLU A:108 , HIS A:111 , PHE A:172 , GLU A:202BINDING SITE FOR RESIDUE MN A 1001
02AC2SOFTWAREGLU A:108 , GLU A:168 , GLU A:202 , HIS A:205BINDING SITE FOR RESIDUE MN A 1002
03AC3SOFTWAREASP B:77 , GLU B:108 , HIS B:111 , PHE B:172 , GLU B:202BINDING SITE FOR RESIDUE MN B 1003
04AC4SOFTWAREGLU B:108 , GLU B:168 , GLU B:202 , HIS B:205BINDING SITE FOR RESIDUE MN B 1004
05AC5SOFTWAREASP C:77 , GLU C:108 , HIS C:111 , GLU C:202BINDING SITE FOR RESIDUE MN C 2001
06AC6SOFTWAREGLU C:108 , GLU C:168 , GLU C:202 , HIS C:205BINDING SITE FOR RESIDUE MN C 2002
07AC7SOFTWAREASP D:77 , GLU D:108 , HIS D:111 , PHE D:172 , GLU D:202BINDING SITE FOR RESIDUE MN D 2003
08AC8SOFTWAREGLU D:108 , GLU D:168 , GLU D:202 , HIS D:205BINDING SITE FOR RESIDUE MN D 2004
09AC9SOFTWAREHOH C:3073 , HOH C:3147 , HOH C:3174 , HOH D:2037 , HOH D:2064BINDING SITE FOR RESIDUE MN C 3001
10BC1SOFTWAREGLU C:222 , GLU C:226BINDING SITE FOR RESIDUE MN C 3002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KGP)

(-) 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:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgpa_ A: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgpA00 A:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgp A   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      


Chain B from PDB  Type:PROTEIN  Length:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgpb_ B: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgpB00 B:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgp B   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      


Chain C from PDB  Type:PROTEIN  Length:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgpc_ C: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgpC00 C:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgp C   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      


Chain D from PDB  Type:PROTEIN  Length:296
 aligned with O69274_CORAM | O69274 from UniProtKB/TrEMBL  Length:329

    Alignment length:296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
         O69274_CORAM     2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
               SCOP domains d1kgpd_ D: Ribonucleotide reductase R2                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1kgpD00 D:2-297 Ribonucleotide Reductase, subunit A                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) -----------Ribonuc_red_sm-1kgpD01 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (1)
           Pfam domains (2) -----------Ribonuc_red_sm-1kgpD02 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (2)
           Pfam domains (3) -----------Ribonuc_red_sm-1kgpD03 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (3)
           Pfam domains (4) -----------Ribonuc_red_sm-1kgpD04 D:13-291                                                                                                                                                                                                                                                        ------ Pfam domains (4)
         Sec.struct. author ...hhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgp D   2 SNEYDEYIANHTDPVKAINWNVIPDEKDLEVWDRLTGNFWLPEKIPVSNDIQSWNKMTPQEQLATMRVFTGLTLLDTIQGTVGAISLLPDAETMHEEAVYTNIAFMESVHAKSYSNIFMTLASTPQINEAFRWSEENENLQRKAKIIMSYYNGDDPLKKKVASTLLESFLFYSGFYLPMYLSSRAKLTNTADIIRLIIRDESVHGYYIGYKYQQGVKKLSEAEQEEYKAYTFDLMYDLYENEIEYTEDIYDDLGWTEDVKRFLRYNANKALNNLGYEGLFPTDETKVSPAILSSLS 297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O69274_CORAM | O69274)
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:0009263    deoxyribonucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of 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.
cellular component
    GO:0005971    ribonucleoside-diphosphate reductase complex    An enzyme complex composed of 2-4 or more subunits, which usually contains nonheme iron and requires ATP for catalysis. Catalyzes the formation of 2'-deoxyribonucleoside diphosphate from ribonucleoside diphosphate, using either thioredoxin disulfide or glutaredoxin disulfide as an acceptor.

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 Related Entries

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

UniProtKB/TrEMBL
        O69274_CORAM | O69274: 1kgn 1kgo 1oqu 3dhz 3mjo

(-) Related Entries Specified in the PDB File

1kgn 1KGN CONTAINS R2F IN ITS OXIDISED, FE3+ CONTAINING, FORM.
1kgo 1KGO CONTAINS R2F WITH FE2+.