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(-) Description

Title :  RIBONUCLEOTIDE REDUCTASE Y731NO2Y MODIFIED R1 SUBUNIT OF E. COLI TO 2.1 A RESOLUTION
 
Authors :  K. Yokoyama, U. Uhlin, J. Stubbe
Date :  31 Mar 10  (Deposition) - 14 Apr 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D,E,F,P
Biol. Unit 1:  A,B,D,E  (3x)
Biol. Unit 2:  C,F  (6x)
Biol. Unit 3:  P  (1x)
Keywords :  Oxidoreductase, Dna Replication, Allosteric Enzyme, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yokoyama, U. Uhlin, J. Stubbe
Site-Specific Incorporation Of 3-Nitrotyrosine As A Probe Of Pk(A) Perturbation Of Redox-Active Tyrosines In Ribonucleotide Reductase.
J. Am. Chem. Soc. V. 132 8385 2010
PubMed-ID: 20518462  |  Reference-DOI: 10.1021/JA101097P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT ALPHA
    Chains: A, B, C
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBADMYCHISA
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-761
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: SITE SPECIFIC INCORPORATION OF 3- NITROTYROSINE AT POSITION 731
    Strain: K-12
    Synonym: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 R1 SUBUNIT, RIBONUCLEOTIDE REDUCTASE 1, PROTEIN B1, RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT
 
Molecule 2 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 SUBUNIT BETA
    Chains: D, E, F, P
    Fragment: RIBONUCLEOTIDE REDUCTASE R2-PEPTIDE, RESIDUES 357-376
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synonym: RIBONUCLEOTIDE REDUCTASE 1, PROTEIN B2, PROTEIN R2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFP
Biological Unit 1 (3x): AB DE  
Biological Unit 2 (6x):   C  F 
Biological Unit 3 (1x):       P

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NIY3Mod. Amino AcidMETA-NITRO-TYROSINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1NIY6Mod. Amino AcidMETA-NITRO-TYROSINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1NIY6Mod. Amino AcidMETA-NITRO-TYROSINE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NIY-1Mod. Amino AcidMETA-NITRO-TYROSINE

(-) Sites  (0, 0)

(no "Site" information available for 2XAP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_ECOLI5-95
 
 		  3A:5-95
B:5-95
C:5-95
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_ECOLI599-621
 
 		  3A:599-621
B:599-621
C:599-621
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_ECOLI5-95
 
 		  6A:5-95
B:5-95
-
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_ECOLI599-621
 
 		  6A:599-621
B:599-621
-
Biological Unit 2 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_ECOLI5-95
 
 		  6-
-
C:5-95
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_ECOLI599-621
 
 		  6-
-
C:599-621
Biological Unit 3 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_ECOLI5-95
 
 		  0-
-
-
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_ECOLI599-621
 
 		  0-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2XAP)

(-) 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:728
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:734
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
           RIR1_ECOLI     4 NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eee.hhhhhhhhhhhhhh.....hhhhhhhhhhh.....eehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..ee.hhhhhhhh.........eeeee...hhhhhhhhhhhhhhhhh...eeeee..........------...hhhhhhhhhhhhhh..........eeeeeee....hhhhhhh......hhhhh....eeeeeehhhhhhhhhhh.eeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh.eeeee.hhhhhh....................................ee.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.hhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhh............hhhhhhh............eeee......eeee..hhhhhh....hhhhh..hhhhhhhhhhhhh.........eeehhhhhhhhheehhhhhhhhhhhhhh...ee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ATP_CONE  PDB: A:5-95 UniProt: 5-95                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xap A   4 NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSP------FHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYyQNTRDG 737
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   |     -|      283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
                                                                                                                                                                                                                                                                                                 267    274                                                                                                                                                                                                                                                                                                                                                                                                                                                                      731-NIY  


Chain B from PDB  Type:PROTEIN  Length:728
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:734
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
           RIR1_ECOLI     4 NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eee.hhhhhhhhhhhhh......hhhhhhhhhhh.....eehhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..ee.hhhhhhhh.........eeeee...hhhhhhhhhhhhhhhhh...eeeee..........------...hhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhh......hhhhh....eeeeeehhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh.eeeee.hhhhhh....................................ee.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.hhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhh............hhhhhhh............eeee......eeee..hhhhhh....hhhhh..hhhhhhhhhhhhhhh.......eeehhhhhhhhheehhhhhhhhhhhhhh...ee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ATP_CONE  PDB: B:5-95 UniProt: 5-95                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xap B   4 NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSP------FHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYyQNTRDG 737
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   |     -|      283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
                                                                                                                                                                                                                                                                                                 267    274                                                                                                                                                                                                                                                                                                                                                                                                                                                                      731-NIY  


Chain C from PDB  Type:PROTEIN  Length:728
 aligned with RIR1_ECOLI | P00452 from UniProtKB/Swiss-Prot  Length:761

    Alignment length:734
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
           RIR1_ECOLI     4 NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDG 737
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -ATP-cone-2xapC04 C:5-92                                                                 ------------------------------------------------Ribonuc_red_lgN-2xapC07 C:141-220                                               -Ribonuc_red_lgC-2xapC01 C:222-732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ----- Pfam domains (1)
           Pfam domains (2) -ATP-cone-2xapC05 C:5-92                                                                 ------------------------------------------------Ribonuc_red_lgN-2xapC08 C:141-220                                               -Ribonuc_red_lgC-2xapC02 C:222-732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ----- Pfam domains (2)
           Pfam domains (3) -ATP-cone-2xapC06 C:5-92                                                                 ------------------------------------------------Ribonuc_red_lgN-2xapC09 C:141-220                                               -Ribonuc_red_lgC-2xapC03 C:222-732                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              ----- Pfam domains (3)
         Sec.struct. author ..eee.....eee.hhhhhhhhhhhhhh.....hhhhhhhhhhh.....eehhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..ee.hhhhhhhh.........eeeee...hhhhhhhhhhhhhhhhh...eeeee..........------....hhhhhhhhhhhhh...........eeeeee....hhhhhhh......hhhhh....eeeeeehhhhhhhhhh..eeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh.eeeeehhhhhhh....................................ee.eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeehhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.hhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhh............hhhhhhh............eeee......eeee..hhhhhh....hhhhh..hhhhhhhhhhhhhhh.......eeehhhhhhhhheehhhhhhhhhhhhhh...ee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ATP_CONE  PDB: C:5-95 UniProt: 5-95                                                        -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xap C   4 NLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFYDGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPPALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQLEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAVSTFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQRAGIGINAGRIRALGSP------FHTGCIPFYKHFQTAVKSCSQGGVRGGAATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKGEDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFSLMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLEIALPTKPLNDVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPIPAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYYLLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWEALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDGILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYDPSRFPSGKVPMQQLLKDLLTAYKFGVKTLYyQNTRDG 737
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   |     -|      283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733    
                                                                                                                                                                                                                                                                                                 267    274                                                                                                                                                                                                                                                                                                                                                                                                                                                                      731-NIY  


Chain D from PDB  Type:PROTEIN  Length:16
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:16
                                   370      
           RIR2_ECOLI   361 QIDSEVDTDDLSNFQL 376
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .ee...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2xap D 360 QIDSEVDTDDLSNFQL 375
                                   369      


Chain E from PDB  Type:PROTEIN  Length:16
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:16
                                   370      
           RIR2_ECOLI   361 QIDSEVDTDDLSNFQL 376
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .ee...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2xap E 360 QIDSEVDTDDLSNFQL 375
                                   369      


Chain F from PDB  Type:PROTEIN  Length:16
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:16
                                   370      
           RIR2_ECOLI   361 QIDSEVDTDDLSNFQL 376
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .ee...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 2xap F 360 QIDSEVDTDDLSNFQL 375
                                   369      


Chain P from PDB  Type:PROTEIN  Length:3
 aligned with RIR2_ECOLI | P69924 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:3
           RIR2_ECOLI   357 YLV 359
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2xap P   1 YLV   3
   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  (0, 0)

(no "SCOP Domain" information available for 2XAP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XAP)

(-) Pfam Domains  (3, 9)

Asymmetric Unit
(-)
Clan: PFL-like (29)
(-)
Clan: no clan defined [family: ATP-cone] (16)
(-)
Clan: no clan defined [family: Ribonuc_red_lgN] (22)

(-) Gene Ontology  (17, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RIR1_ECOLI | P00452)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

Chain D,E,F,P   (RIR2_ECOLI | P69924)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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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  RIR2_ECOLI | P69924
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIR1_ECOLI | P00452: 1qfn 1r1r 1rlr 2r1r 2x0x 2xak 2xav 2xaw 2xax 2xay 2xaz 2xo4 2xo5 3r1r 3uus 4erm 4erp 4r1r 5cns 5cnt 5cnu 5cnv 5r1r 6r1r 7r1r
        RIR2_ECOLI | P69924: 1av8 1biq 1jpr 1jqc 1mrr 1mxr 1pfr 1pim 1piu 1piy 1piz 1pj0 1pj1 1pm2 1r1r 1r65 1rib 1rnr 1rsr 1rsv 1xik 1yfd 2alx 2av8 2r1r 2x0x 2xak 2xav 2xaw 2xax 2xay 2xaz 2xo4 2xo5 2xof 3r1r 3uus 4erm 4erp 4r1r 5ci2 5ci3 5cns 5cnt 5cnu 5cnv 5r1r 6r1r 7r1r

(-) Related Entries Specified in the PDB File

1qfn GLUTAREDOXIN-1-RIBONUCLEOTIDE REDUCTASE B1 MIXED DISULFIDE BOND
1r1r RIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH AREDUCED ACTIVE SITE FROM ESCHERICHIA COLI
1rlr STRUCTURE OF RIBONUCLEOTIDE REDUCTASE PROTEIN R1
2r1r RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH DTTP OCCUPYING THESPECIFICITY SITE FROM ESCHERICHIA COLI
2x0x RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT OF E. COLI TO 2.3 A RESOLUTION
2xak RIBONUCLEOTIDE REDUCTASE Y730NO2Y MODIFIED R1 SUBUNIT OF E. COLI
2xav RIBONUCLEOTIDE REDUCTASE Y731NO2Y AND Y730F MODIFIED R1 SUBUNIT OF E. COLI
2xaw RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND Y731F MODIFIED R1 SUBUNIT OF E. COLI
2xax RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND Y731A MODIFIED R1 SUBUNIT OF E. COLI
2xay RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND C439A MODIFIED R1 SUBUNIT OF E. COLI
2xaz RIBONUCLEOTIDE REDUCTASE Y730NO2Y AND C439S MODIFIED R1 SUBUNIT OF E. COLI
3r1r RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYINGTHE ACTIVITY SITE FROM ESCHERICHIA COLI
4r1r RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH SUBSTRATE, GDP ANDEFFECTOR DTTP FROM ESCHERICHIA COLI
5r1r RIBONUCLEOTIDE REDUCTASE E441A MUTANT R1 PROTEIN FROMESCHERICHIA COLI
6r1r RIBONUCLEOTIDE REDUCTASE E441D MUTANT R1 PROTEIN FROMESCHERICHIA COLI
7r1r RIBONUCLEOTIDE REDUCTASE E441Q MUTANT R1 PROTEIN FROMESCHERICHIA COLI