PBP2_STRR6
ID PBP2_STRR6 Reviewed; 680 AA.
AC P0A3M6; P10524;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 25-MAY-2022, entry version 96.
DE RecName: Full=Penicillin-binding protein 2B;
DE Short=PBP2b;
DE AltName: Full=Peptidoglycan transpeptidase {ECO:0000303|PubMed:23873916};
GN Name=penA {ECO:0000303|PubMed:2798106}; Synonyms=pbp2b;
GN OrderedLocusNames=spr1517;
OS Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=171101;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=2798106; DOI=10.1093/nar/17.18.7518;
RA Dowson C.G., Hutchison A., Spratt B.G.;
RT "Nucleotide sequence of the penicillin-binding protein 2B gene of
RT Streptococcus pneumoniae strain R6.";
RL Nucleic Acids Res. 17:7518-7518(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=11544234; DOI=10.1128/jb.183.19.5709-5717.2001;
RA Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S.,
RA DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C.,
RA Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J.,
RA Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M.,
RA McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B.,
RA Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y.,
RA Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R.,
RA Rosteck P.R. Jr., Skatrud P.L., Glass J.I.;
RT "Genome of the bacterium Streptococcus pneumoniae strain R6.";
RL J. Bacteriol. 183:5709-5717(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 195-680.
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=2654541; DOI=10.1111/j.1365-2958.1989.tb00108.x;
RA Dowson C.G., Hutchison A., Spratt B.G.;
RT "Extensive re-modelling of the transpeptidase domain of penicillin-binding
RT protein 2B of a penicillin-resistant South African isolate of Streptococcus
RT pneumoniae.";
RL Mol. Microbiol. 3:95-102(1989).
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=8454182; DOI=10.1111/j.1574-6968.1993.tb05954.x;
RA Kell C.M., Sharma U.K., Dowson C.G., Town C., Balganesh T.S., Spratt B.G.;
RT "Deletion analysis of the essentiality of penicillin-binding proteins 1A,
RT 2B and 2X of Streptococcus pneumoniae.";
RL FEMS Microbiol. Lett. 106:171-175(1993).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=R6 / R704;
RX PubMed=23873916; DOI=10.1128/jb.00184-13;
RA Berg K.H., Stamsaas G.A., Straume D., Haavarstein L.S.;
RT "Effects of low PBP2b levels on cell morphology and peptidoglycan
RT composition in Streptococcus pneumoniae R6.";
RL J. Bacteriol. 195:4342-4354(2013).
RN [6]
RP SUBUNIT.
RC STRAIN=R6 / R704;
RX PubMed=28710862; DOI=10.1111/mmi.13748;
RA Stamsaas G.A., Straume D., Ruud Winther A., Kjos M., Frantzen C.A.,
RA Haavarstein L.S.;
RT "Identification of EloR (Spr1851) as a regulator of cell elongation in
RT Streptococcus pneumoniae.";
RL Mol. Microbiol. 105:954-967(2017).
RN [7] {ECO:0007744|PDB:2WAD, ECO:0007744|PDB:2WAE, ECO:0007744|PDB:2WAF}
RP X-RAY CRYSTALLOGRAPHY (3.29 ANGSTROMS) OF 36-680, FUNCTION, PROBABLE ACTIVE
RP SITE, AND DOMAIN.
RC STRAIN=5204, and ATCC BAA-255 / R6;
RX PubMed=19233207; DOI=10.1016/j.jmb.2009.02.024;
RA Contreras-Martel C., Dahout-Gonzalez C., Martins Ados S., Kotnik M.,
RA Dessen A.;
RT "PBP active site flexibility as the key mechanism for beta-lactam
RT resistance in pneumococci.";
RL J. Mol. Biol. 387:899-909(2009).
CC -!- FUNCTION: A transpeptidase that forms peptide cross-links between
CC adjacent glycan strands in cell wall peptidoglycan (PG). Part of the
CC elongasome machinery that synthesizes peripheral PG.
CC {ECO:0000305|PubMed:19233207, ECO:0000305|PubMed:23873916}.
CC -!- SUBUNIT: Interacts with MreC in the elongasome.
CC {ECO:0000269|PubMed:28710862}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Single-pass membrane
CC protein {ECO:0000255}. Note=Localizes to the midcell division sites,
CC colocalizes with StkP. {ECO:0000250|UniProtKB:A0A0H2ZQ75}.
CC -!- DOMAIN: Comparison of drug-sensitive and drug-resistant protein
CC structures shows the active site is highly flexible.
CC {ECO:0000269|PubMed:19233207}.
CC -!- DISRUPTION PHENOTYPE: Essential, it cannot be deleted (PubMed:8454182).
CC Cells depleted of PBP2b continue to grow more slowly than wild-type
CC until at least 12 hours after expression stops. Cells form very long
CC chains and have an altered shape, becoming lentil-like rather than
CC ellipsoid. Cells are more sensitive to amidase and have an altered stem
CC peptide composition (PubMed:23873916). {ECO:0000269|PubMed:23873916,
CC ECO:0000269|PubMed:8454182}.
CC -!- MISCELLANEOUS: Structures 2WAD and 2WAE are from strain 5204, a
CC clinical, drug-resistant strain with 58 mutations in compared to strain
CC R6. {ECO:0000269|PubMed:19233207}.
CC -!- SIMILARITY: Belongs to the transpeptidase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL00321.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X16022; CAA34154.1; -; Genomic_DNA.
DR EMBL; AE007317; AAL00321.1; ALT_INIT; Genomic_DNA.
DR EMBL; X13137; CAA31527.1; -; Genomic_DNA.
DR PIR; D98061; D98061.
DR PIR; S06000; S06000.
DR RefSeq; NP_359110.1; NC_003098.1.
DR RefSeq; WP_001224867.1; NC_003098.1.
DR PDB; 2WAD; X-ray; 2.18 A; A/B/C=36-680.
DR PDB; 2WAE; X-ray; 2.26 A; A=36-680.
DR PDB; 2WAF; X-ray; 3.29 A; A=36-680.
DR PDBsum; 2WAD; -.
DR PDBsum; 2WAE; -.
DR PDBsum; 2WAF; -.
DR AlphaFoldDB; P0A3M6; -.
DR SMR; P0A3M6; -.
DR STRING; 171101.spr1517; -.
DR ChEMBL; CHEMBL4296322; -.
DR DrugBank; DB01163; Amdinocillin.
DR DrugBank; DB00415; Ampicillin.
DR DrugBank; DB08795; Azidocillin.
DR DrugBank; DB01140; Cefadroxil.
DR DrugBank; DB00456; Cefalotin.
DR DrugBank; DB01066; Cefditoren.
DR DrugBank; DB00493; Cefotaxime.
DR DrugBank; DB01331; Cefoxitin.
DR DrugBank; DB01212; Ceftriaxone.
DR DrugBank; DB00567; Cephalexin.
DR DrugBank; DB03313; Cephalosporin C.
DR DrugBank; DB00485; Dicloxacillin.
DR DrugBank; DB00739; Hetacillin.
DR DrugBank; DB01603; Meticillin.
DR DrugBank; DB00607; Nafcillin.
DR DrugBank; DB00713; Oxacillin.
DR DrugBank; DB00319; Piperacillin.
DR MEROPS; X52.001; -.
DR EnsemblBacteria; AAL00321; AAL00321; spr1517.
DR KEGG; spr:spr1517; -.
DR PATRIC; fig|171101.6.peg.1637; -.
DR eggNOG; COG0768; Bacteria.
DR HOGENOM; CLU_009289_7_0_9; -.
DR EvolutionaryTrace; P0A3M6; -.
DR Proteomes; UP000000586; Chromosome.
DR GO; GO:0005887; C:integral component of plasma membrane; IBA:GO_Central.
DR GO; GO:0008658; F:penicillin binding; IBA:GO_Central.
DR GO; GO:0071972; F:peptidoglycan L,D-transpeptidase activity; IBA:GO_Central.
DR GO; GO:0071555; P:cell wall organization; IBA:GO_Central.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR Gene3D; 3.40.710.10; -; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR005311; PBP_dimer.
DR InterPro; IPR036138; PBP_dimer_sf.
DR InterPro; IPR001460; PCN-bd_Tpept.
DR Pfam; PF03717; PBP_dimer; 1.
DR Pfam; PF00905; Transpeptidase; 1.
DR SUPFAM; SSF56519; SSF56519; 1.
DR SUPFAM; SSF56601; SSF56601; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; Cell membrane; Cell shape;
KW Cell wall biogenesis/degradation; Membrane; Peptidoglycan synthesis;
KW Reference proteome; Transmembrane; Transmembrane helix.
FT CHAIN 1..680
FT /note="Penicillin-binding protein 2B"
FT /id="PRO_0000195456"
FT TOPO_DOM 1..8
FT /note="Cytoplasmic"
FT /evidence="ECO:0000305"
FT TRANSMEM 9..29
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 30..680
FT /note="Extracellular"
FT /evidence="ECO:0000305"
FT REGION 314..680
FT /note="Transpeptidase domain"
FT /evidence="ECO:0000305|PubMed:19233207"
FT ACT_SITE 386
FT /note="Acyl-ester intermediate"
FT /evidence="ECO:0000250|UniProtKB:P0AD65,
FT ECO:0000305|PubMed:19233207"
FT CONFLICT 37
FT /note="L -> F (in Ref. 1; CAA34154)"
FT /evidence="ECO:0000305"
FT CONFLICT 115..117
FT /note="QLA -> AG (in Ref. 1; CAA34154)"
FT /evidence="ECO:0000305"
FT STRAND 53..58
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 72..83
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 90..101
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 113..120
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 124..131
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 150..160
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 171..182
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 200..208
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 216..225
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 231..234
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 240..242
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 246..255
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 267..271
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 273..276
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 277..284
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 307..311
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 314..333
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 334..339
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 342..348
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 350..352
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 354..363
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 365..367
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 370..372
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 376..379
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 385..388
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 389..398
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 407..410
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 424..428
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 431..435
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 436..441
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 445..456
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 468..470
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 471..484
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 485..488
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 494..496
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 509..515
FT /evidence="ECO:0007829|PDB:2WAF"
FT TURN 516..518
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 519..523
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 525..536
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 539..542
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 545..553
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 557..565
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 570..573
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 578..593
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 602..605
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 613..616
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 619..621
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 629..631
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 634..638
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 640..642
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 645..650
FT /evidence="ECO:0007829|PDB:2WAF"
FT STRAND 653..655
FT /evidence="ECO:0007829|PDB:2WAF"
FT HELIX 661..674
FT /evidence="ECO:0007829|PDB:2WAF"
SQ SEQUENCE 680 AA; 73873 MW; 56BF2C1AA9B54C3B CRC64;
MRKFNSHSIP IRLNLLFSIV ILLFMTIIGR LLYMQVLNKD FYEKKLASAS QTKITSSSAR
GEIYDASGKP LVENTLKQVV SFTRSNKMTA TDLKETAKKL LTYVSISSPN LTERQLADYY
LADPEIYKKI VEALPSEKRL DSDGNRLSES ELYNNAVDSV QTSQLNYTED EKKEIYLFSQ
LNAVGNFATG TIATDPLNDS QVAVIASISK EMPGISISTS WDRKVLETSL SSIVGSVSSE
KAGLPAEEAE AYLKKGYSLN DRVGTSYLEK QYEETLQGKR SVKEIHLDKY GNMESVDTIE
EGSKGNNIKL TIDLAFQDSV DALLKSYFNS ELENGGAKYS EGVYAVALNP KTGAVLSMSG
IKHDLKTGEL TPDSLGTVTN VFVPGSVVKA ATISSGWENG VLSGNQTLTD QSIVFQGSAP
INSWYTQAYG SFPITAVQAL EYSSNTYMVQ TALGLMGQTY QPNMFVGTSN LESAMEKLRS
TFGEYGLGTA TGIDLPDEST GFVPKEYSFA NYITNAFGQF DNYTPMQLAQ YVATIANNGV
RVAPRIVEGI YGNNDKGGLG DLIQQLQPTE MNKVNISDSD MSILHQGFYQ VAHGTSGLTT
GRAFSNGALV SISGKTGTAE SYVADGQQAT NTNAVAYAPS DNPQIAVAVV FPHNTNLTNG
VGPSIARDII NLYQKYHPMN
