CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001770
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Ribonucleoside-diphosphate reductase 1 subunit alpha 
Protein Synonyms/Alias
 Protein B1; Ribonucleoside-diphosphate reductase 1 R1 subunit; Ribonucleotide reductase 1 
Gene Name
 nrdA 
Gene Synonyms/Alias
 dnaF; b2234; JW2228 
Created Date
 July 27, 2013 
Organism
 Escherichia coli (strain K12) 
NCBI Taxa ID
 83333 
Lysine Modification
Position
Peptide
Type
References
21TERINLDKIHRVLDWacetylation[1, 2]
54IQFYDGIKTSDIHETacetylation[2]
64DIHETIIKAAADLISacetylation[2]
108ALYDHVVKMVEMGKYacetylation[2]
114VKMVEMGKYDNHLLEacetylation[2]
129DYTEEEFKQMDTFIDacetylation[2]
154AVKQLEGKYLVQNRVacetylation[2]
283TGCIPFYKHFQTAVKacetylation[1, 2, 3]
341DYGVQINKLMYTRLLacetylation[2]
381EFERLYTKYEKDDSIacetylation[2]
384RLYTKYEKDDSIRKQacetylation[1, 2]
504DYPIPAAKRGAMGRRacetylation[2]
542SANNLTHKTFEAIQYacetylation[2]
560KASNELAKEQGACPWacetylation[2]
584ILPIDTYKKDLDTIAacetylation[2]
585LPIDTYKKDLDTIANacetylation[2]
648YVSIKASKDGILRQVacetylation[2]
708PSRFPSGKVPMQQLLacetylation[1]
716VPMQQLLKDLLTAYKacetylation[2]
723KDLLTAYKFGVKTLYacetylation[2]
Reference
 [1] Comprehensive profiling of protein lysine acetylation in Escherichia coli.
 Zhang K, Zheng S, Yang JS, Chen Y, Cheng Z.
 J Proteome Res. 2013 Feb 1;12(2):844-51. [PMID: 23294111]
 [2] Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli.
 Weinert BT, Iesmantavicius V, Wagner SA, Schölz C, Gummesson B, Beli P, Nyström T, Choudhary C.
 Mol Cell. 2013 Jul 25;51(2):265-72. [PMID: 23830618]
 [3] Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli.
 Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y.
 Mol Cell Proteomics. 2009 Feb;8(2):215-25. [PMID: 18723842] 
Functional Description
 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide. It also provides redox- active cysteines. 
Sequence Annotation
 DOMAIN 5 95 ATP-cone.
 REGION 15 21 Allosteric activator binding.
 REGION 224 225 Substrate binding (By similarity).
 REGION 437 441 Substrate binding (By similarity).
 REGION 621 625 Substrate binding.
 ACT_SITE 437 437 Proton acceptor.
 ACT_SITE 439 439 Cysteine radical intermediate.
 ACT_SITE 441 441 Proton acceptor.
 BINDING 9 9 Allosteric activator.
 BINDING 55 55 Allosteric activator.
 BINDING 91 91 Allosteric activator.
 BINDING 209 209 Substrate.
 BINDING 253 253 Substrate; via amide nitrogen (By
 MOD_RES 283 283 N6-acetyllysine.
 DISULFID 225 462 Redox-active.  
Keyword
 3D-structure; Acetylation; Allosteric enzyme; Alternative initiation; ATP-binding; Complete proteome; Direct protein sequencing; Disulfide bond; DNA replication; Nucleotide-binding; Oxidoreductase; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 761 AA 
Protein Sequence
MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE 60
TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAYGQFEPP ALYDHVVKMV EMGKYDNHLL 120
EDYTEEEFKQ MDTFIDHDRD MTFSYAAVKQ LEGKYLVQNR VTGEIYESAQ FLYILVAACL 180
FSNYPRETRL QYVKRFYDAV STFKISLPTP IMSGVRTPTR QFSSCVLIEC GDSLDSINAT 240
SSAIVKYVSQ RAGIGINAGR IRALGSPIRG GEAFHTGCIP FYKHFQTAVK SCSQGGVRGG 300
AATLFYPMWH LEVESLLVLK NNRGVEGNRV RHMDYGVQIN KLMYTRLLKG EDITLFSPSD 360
VPGLYDAFFA DQEEFERLYT KYEKDDSIRK QRVKAVELFS LMMQERASTG RIYIQNVDHC 420
NTHSPFDPAI APVRQSNLCL EIALPTKPLN DVNDENGEIA LCTLSAFNLG AINNLDELEE 480
LAILAVRALD ALLDYQDYPI PAAKRGAMGR RTLGIGVINF AYYLAKHGKR YSDGSANNLT 540
HKTFEAIQYY LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDTI ANEPLHYDWE 600
ALRESIKTHG LRNSTLSALM PSETSSQISN ATNGIEPPRG YVSIKASKDG ILRQVVPDYE 660
HLHDAYELLW EMPGNDGYLQ LVGIMQKFID QSISANTNYD PSRFPSGKVP MQQLLKDLLT 720
AYKFGVKTLY YQNTRDGAED AQDDLVPSIQ DDGCESGACK I 761 
Gene Ontology
 GO:0005971; C:ribonucleoside-diphosphate reductase complex; IDA:EcoliWiki.
 GO:0005524; F:ATP binding; IDA:EcoliWiki.
 GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IDA:EcoCyc.
 GO:0009263; P:deoxyribonucleotide biosynthetic process; IDA:EcoliWiki.
 GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
 GO:0015949; P:nucleobase-containing small molecule interconversion; IDA:EcoliWiki. 
Interpro
 IPR005144; ATP-cone.
 IPR013346; NrdE_NrdA.
 IPR000788; RNR_lg_C.
 IPR013509; RNR_lsu_N.
 IPR008926; RNR_R1-su_N. 
Pfam
 PF03477; ATP-cone
 PF02867; Ribonuc_red_lgC
 PF00317; Ribonuc_red_lgN 
SMART
  
PROSITE
 PS51161; ATP_CONE
 PS00089; RIBORED_LARGE 
PRINTS
 PR01183; RIBORDTASEM1.