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(-) Description

Title :  LOW RESOLUTION X-RAY CRYSTAL STRUCTURE OF YEAST RNR1P WITH DATP BOUND IN THE A-SITE
 
Authors :  J. W. Fairman, S. R. Wijerathna, C. G. Dealwis
Date :  19 Oct 10  (Deposition) - 23 Feb 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  6.61
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ribonucleotide Reductase, Oxidoreductase, Nucleotide Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. W. Fairman, S. R. Wijerathna, M. F. Ahmad, H. Xu, R. Nakano, S. Jha, J. Prendergast, R. M. Welin, S. Flodin, A. Roos, P. Nordlund, Z. Li, T. Walz, C. G. Dealwis
Structural Basis For Allosteric Regulation Of Human Ribonucleotide Reductase By Nucleotide-Induced Oligomerization.
Nat. Struct. Mol. Biol. V. 18 316 2011
PubMed-ID: 21336276  |  Reference-DOI: 10.1038/NSMB.2007

(-) Compounds

Molecule 1 - RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN 1
    Chains: A, B, C, D
    EC Number: 1.17.4.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21-DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RNR1, CRT7, RIR1, SDS12, YER070W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: RIBONUCLEOTIDE REDUCTASE R1 SUBUNIT 1, RIBONUCLEOTIDE REDUCTASE LARGE SUBUNIT 1

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3PAW)

(-) Sites  (0, 0)

(no "Site" information available for 3PAW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr A:401 -Pro A:402
2Thr B:401 -Pro B:402
3Thr C:401 -Pro C:402
4Thr D:401 -Pro D:402

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_YEAST1-92
 
 
 		  4A:1-92
B:1-92
C:1-92
D:1-92
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_YEAST585-607
 
 
 		  4A:585-607
B:585-607
C:585-607
D:585-607
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_YEAST1-92
 
 
 		  2A:1-92
B:1-92
-
-
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_YEAST585-607
 
 
 		  2A:585-607
B:585-607
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_CONEPS51161 ATP-cone domain profile.RIR1_YEAST1-92
 
 
 		  2-
-
C:1-92
D:1-92
2RIBORED_LARGEPS00089 Ribonucleotide reductase large subunit signature.RIR1_YEAST585-607
 
 
 		  2-
-
C:585-607
D:585-607

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YER070W1YER070W.1V:298948-3016142667RIR1_YEAST1-8888884A:1-746 (gaps)
B:1-746 (gaps)
C:1-746 (gaps)
D:1-746 (gaps)		746
746
746
746

(-) 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:739
 aligned with RIR1_YEAST | P21524 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
           RIR1_YEAST     1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.......ee.......................hhhhhh.hhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..hhhhhh.............................................hhhhhh................hhhhh...........hhhhhhhhhhhhh...eee.................................hhhhhhhh......eeee.............................................eeee.............................ee...hhhhhhhhh....eeee.hhhh.......................eeee....hhhhhhhhhhhh........hhhhhh...............................eeee...................hhhhhhhhhhhhhh...........hhhhhh.......eeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...................hhhhh................hhhhhhhhhh.................hhhhhh..............-------...................hhhhhh...................................................ee...........................ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: A:1-92 UniProt: 1-92                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-746 (gaps) UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 3paw A   1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYS-------FQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               630     638                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:739
 aligned with RIR1_YEAST | P21524 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
           RIR1_YEAST     1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................................hhhhhhhhh...........hhhhhh.........hhhhhhhhhhhhhh...............................hhhhhh..hhhhhh.....hhhhh.hhhhhh................hhhhhhhhh...........hhhhhhhhhh..ee..hhhhhh...................hhhhhhhhhhhh........................................hhhhhh..............eee............................eeeee.............ee.............hhhhhh.............ee...hhhhhhhhhh......eeee........................................eee.................hhhhhhhhhhhhhhh...........hhhhhh..........eehhhhhhh.......hhhhhhhhhhh...hhhhhh..................hhhhhh...................hhhhhh.................hhhhhh...........ee.-------..eehhhhhhhhhh.........................hhhhhh..........hhhhh................ee.............hhhhhh........ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: B:1-92 UniProt: 1-92                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-746 (gaps) UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 3paw B   1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYS-------FQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               630     638                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:739
 aligned with RIR1_YEAST | P21524 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
           RIR1_YEAST     1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................hhhhhhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhh.........hhhhhh.....................hhhhh...................hhhhhhhhhhh...........hhhhhh..........hhhhhhhhhhhhhh..ee.hhhhhhhh.........ee..........hhhhhh...........eeeee...........................hhhhhh.............eeee......hhhhhh...............eeee..hhhhhhh...........................................hhhhhhhhhhh........eehhhhhh...................................ee.................hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhh.......hhhhhhh.........hhhhhh.....hhhhhh.....hhhhhh...............................hhhhhhhhh................hhhhhh..............-------.......................................hhhhhhhh.............hhhhh...........ee.............hhhhhh...eee..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: C:1-92 UniProt: 1-92                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-746 (gaps) UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 3paw C   1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYS-------FQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               630     638                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:739
 aligned with RIR1_YEAST | P21524 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:746
                                    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       640       650       660       670       680       690       700       710       720       730       740      
           RIR1_YEAST     1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSRRVLSGEFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ATP-cone-3pawD05 D:1-89                                                                  ---------------------------------------------------Ribonuc_red_lgN-3pawD09 D:141-213                                        -Ribonuc_red_lgC-3pawD01 D:215-743                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                --- Pfam domains (1)
           Pfam domains (2) ATP-cone-3pawD06 D:1-89                                                                  ---------------------------------------------------Ribonuc_red_lgN-3pawD10 D:141-213                                        -Ribonuc_red_lgC-3pawD02 D:215-743                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                --- Pfam domains (2)
           Pfam domains (3) ATP-cone-3pawD07 D:1-89                                                                  ---------------------------------------------------Ribonuc_red_lgN-3pawD11 D:141-213                                        -Ribonuc_red_lgC-3pawD03 D:215-743                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                --- Pfam domains (3)
           Pfam domains (4) ATP-cone-3pawD08 D:1-89                                                                  ---------------------------------------------------Ribonuc_red_lgN-3pawD12 D:141-213                                        -Ribonuc_red_lgC-3pawD04 D:215-743                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                --- Pfam domains (4)
         Sec.struct. author ......................................hhhhh........hhhhhh.hhhhhh..........hhhhhhhhhh................................hhhhhhh..............hhhhh.hhhhhhhhhhh...........hhhhhhh.............hhhhhhh......ee..................................hhhhh.....................................hhhhh.......................................................hhhhh.....eee................................eee.....................hhhhhhhh...............................eee......ee........ee.......hhhhhh..............hhhhhhhhh....eee..hhhhhhh.......hhhhhhhhh.....................................hhhhh........hhhhhhhhh.................hhhhhhh..............-------..................hhhhh.....................................................ee....hhhhhhhhhh.............ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ATP_CONE  PDB: D:1-92 UniProt: 1-92                                                         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RIBORED_LARGE          ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-746 (gaps) UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 3paw D   1 MYVYKRDGRKEPVQFDKITARISRLCYGLDPKHIDAVKVTQRIISGVYEGVTTIELDNLAAETCAYMTTVHPDYATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYS-------FQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ 746
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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               630     638
   Legend:   → Mismatch (orange background)
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 12)

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  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RIR1_YEAST | P21524)
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: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: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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  3paw
    Family and Domain Information: ProDom | SYSTERS
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  RIR1_YEAST | P21524
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  1.17.4.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIR1_YEAST | P21524: 1zyz 1zzd 2cvs 2cvt 2cvu 2cvv 2cvw 2cvx 2cvy 2eud 2zlf 2zlg 3k8t 3rsr 3s87 3s8a 3s8b 3s8c 3tb9 3tba

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3PAW)