MAP1B_PLAF7
ID MAP1B_PLAF7 Reviewed; 517 AA.
AC Q8IJP2;
DT 07-OCT-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=Methionine aminopeptidase 1b {ECO:0000303|PubMed:16983082};
DE EC=3.4.11.18 {ECO:0000255|RuleBase:RU003653, ECO:0000269|PubMed:16983082, ECO:0000269|PubMed:27023914};
DE AltName: Full=PfMetAP1b {ECO:0000303|PubMed:16983082};
GN Name=METAP1b {ECO:0000303|PubMed:16983082};
GN ORFNames=PF3D7_1015300 {ECO:0000312|EMBL:CZT98405.1};
OS Plasmodium falciparum (isolate 3D7).
OC Eukaryota; Sar; Alveolata; Apicomplexa; Aconoidasida; Haemosporida;
OC Plasmodiidae; Plasmodium; Plasmodium (Laverania).
OX NCBI_TaxID=36329 {ECO:0000312|Proteomes:UP000001450};
RN [1] {ECO:0000312|Proteomes:UP000001450}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3D7 {ECO:0000312|Proteomes:UP000001450};
RX PubMed=12368864; DOI=10.1038/nature01097;
RA Gardner M.J., Hall N., Fung E., White O., Berriman M., Hyman R.W.,
RA Carlton J.M., Pain A., Nelson K.E., Bowman S., Paulsen I.T., James K.D.,
RA Eisen J.A., Rutherford K.M., Salzberg S.L., Craig A., Kyes S., Chan M.-S.,
RA Nene V., Shallom S.J., Suh B., Peterson J., Angiuoli S., Pertea M.,
RA Allen J., Selengut J., Haft D., Mather M.W., Vaidya A.B., Martin D.M.A.,
RA Fairlamb A.H., Fraunholz M.J., Roos D.S., Ralph S.A., McFadden G.I.,
RA Cummings L.M., Subramanian G.M., Mungall C., Venter J.C., Carucci D.J.,
RA Hoffman S.L., Newbold C., Davis R.W., Fraser C.M., Barrell B.G.;
RT "Genome sequence of the human malaria parasite Plasmodium falciparum.";
RL Nature 419:498-511(2002).
RN [2] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=16983082; DOI=10.1073/pnas.0604101103;
RA Chen X., Chong C.R., Shi L., Yoshimoto T., Sullivan D.J. Jr., Liu J.O.;
RT "Inhibitors of Plasmodium falciparum methionine aminopeptidase 1b possess
RT antimalarial activity.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:14548-14553(2006).
RN [3] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF CYS-316.
RX PubMed=27023914; DOI=10.1007/s00253-016-7470-3;
RA Calcagno S., Klein C.D.;
RT "N-Terminal methionine processing by the zinc-activated Plasmodium
RT falciparum methionine aminopeptidase 1b.";
RL Appl. Microbiol. Biotechnol. 100:7091-7102(2016).
RN [4] {ECO:0007744|PDB:3S6B}
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 168-517 IN COMPLEX WITH IRON.
RA Wernimont A.K., Artz J.D., Crombet L., Lew J., Weadge J., Arrowsmith C.H.,
RA Edwards A.M., Weigelt J., Bountra C., Hui R., Hills T.;
RT "Crystal structure of methionine aminopeptidase 1b from Plasmodium
RT Falciparum, PF10_0150.";
RL Submitted (MAY-2011) to the PDB data bank.
CC -!- FUNCTION: Cotranslationally removes the N-terminal methionine from
CC nascent proteins (PubMed:16983082, PubMed:27023914). The N-terminal
CC methionine is often cleaved when the second residue in the primary
CC sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or
CC Val) (By similarity). May play an important role in parasite growth
CC during the blood asexual stage (PubMed:16983082).
CC {ECO:0000255|RuleBase:RU003653, ECO:0000269|PubMed:16983082,
CC ECO:0000269|PubMed:27023914}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Release of N-terminal amino acids, preferentially methionine,
CC from peptides and arylamides.; EC=3.4.11.18;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03174,
CC ECO:0000269|PubMed:16983082, ECO:0000269|PubMed:27023914};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03174,
CC ECO:0000269|PubMed:27023914};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03174,
CC ECO:0000269|PubMed:27023914};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03174,
CC ECO:0000269|PubMed:27023914};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_03174,
CC ECO:0000269|PubMed:27023914};
CC Note=Highest activity with zinc and cobalt ions, and low activity with
CC manganese or divalent iron ions (PubMed:27023914). Binds 2 divalent
CC metal cations per subunit. Has a high-affinity and a low affinity
CC metal-binding site. The true nature of the physiological cofactor is
CC under debate. The enzyme is active with cobalt, zinc, manganese or
CC divalent iron ions. Most likely, methionine aminopeptidases function as
CC mononuclear Fe(2+)-metalloproteases under physiological conditions, and
CC the catalytically relevant metal-binding site has been assigned to the
CC histidine-containing high-affinity site (By similarity).
CC {ECO:0000255|HAMAP-Rule:MF_03174, ECO:0000269|PubMed:27023914};
CC -!- ACTIVITY REGULATION: Inhibited by pyrimidine derivative XC11.
CC {ECO:0000269|PubMed:16983082}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=327.3 uM for methionine containing-oligopeptide
CC {ECO:0000269|PubMed:16983082};
CC KM=845.08 uM for Met-Gly-Met-Met peptide (in presence of 1 uM Zn(2+),
CC at 37 degrees Celsius, pH 7.5) {ECO:0000269|PubMed:27023914};
CC KM=1117.7 uM for Met-Gly-Met-Met peptide (in presence of 10 uM
CC Zn(2+), at 37 degrees Celsius, pH 7.5) {ECO:0000269|PubMed:27023914};
CC KM=1662.4 uM for Met-Gly-Met-Met peptide (in presence of 100 uM
CC Zn(2+), at 37 degrees Celsius, pH 7.5) {ECO:0000269|PubMed:27023914};
CC KM=1759 uM for Met-Gly-Met-Met peptide (in presence of 1 uM Co(2+),
CC at 37 degrees Celsius, pH 7.5) {ECO:0000269|PubMed:27023914};
CC KM=1142.4 uM for Met-Gly-Met-Met peptide (in presence of 10 uM
CC Co(2+), at 37 degrees Celsius, pH 7.5) {ECO:0000269|PubMed:27023914};
CC KM=1061.5 uM for Met-Gly-Met-Met peptide (in presence of 100 uM
CC Co(2+), at 37 degrees Celsius, pH 7.5) {ECO:0000269|PubMed:27023914};
CC Note=kcat is 13.9 min(-1) with methionine containing-oligopeptide as
CC substrate (PubMed:16983082). kcat is 552.49 min(-1) in presence of 1
CC uM Zn(2+), 442.48 min(-1) in presence of 10 uM Zn(2+) and 364.30
CC min(-1) in presence of 100 uM Zn(2+), with Met-Gly-Met-Met peptide as
CC substrate (PubMed:27023914). kcat is 1005 min(-1) in presence of 1 uM
CC Co(2+), 583.09 min(-1) in presence of 10 uM Co(2+) and 547.95 min(-1)
CC in presence of 100 uM Co(2+), with Met-Gly-Met-Met peptide as
CC substrate (PubMed:27023914). {ECO:0000269|PubMed:16983082,
CC ECO:0000269|PubMed:27023914};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:27023914};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius (PubMed:27023914). However,
CC has substantial activity at 25 degrees Celsius (PubMed:27023914).
CC {ECO:0000269|PubMed:27023914};
CC -!- SIMILARITY: Belongs to the peptidase M24A family. Methionine
CC aminopeptidase type 1 subfamily. {ECO:0000255|HAMAP-Rule:MF_03174}.
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DR EMBL; LN999944; CZT98405.1; -; Genomic_DNA.
DR RefSeq; XP_001347435.1; XM_001347399.1.
DR PDB; 3S6B; X-ray; 1.95 A; A=168-517.
DR PDBsum; 3S6B; -.
DR AlphaFoldDB; Q8IJP2; -.
DR SMR; Q8IJP2; -.
DR IntAct; Q8IJP2; 2.
DR STRING; 5833.PF10_0150; -.
DR MEROPS; M24.017; -.
DR PRIDE; Q8IJP2; -.
DR EnsemblProtists; CZT98405; CZT98405; PF3D7_1015300.
DR GeneID; 810308; -.
DR KEGG; pfa:PF3D7_1015300; -.
DR VEuPathDB; PlasmoDB:PF3D7_1015300; -.
DR HOGENOM; CLU_015857_2_0_1; -.
DR InParanoid; Q8IJP2; -.
DR OMA; SKMYVMP; -.
DR PhylomeDB; Q8IJP2; -.
DR Proteomes; UP000001450; Chromosome 10.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0070006; F:metalloaminopeptidase activity; IBA:GO_Central.
DR GO; GO:0008235; F:metalloexopeptidase activity; ISS:GeneDB.
DR GO; GO:0035551; P:protein initiator methionine removal involved in protein maturation; IBA:GO_Central.
DR GO; GO:0006508; P:proteolysis; ISS:GeneDB.
DR CDD; cd01086; MetAP1; 1.
DR Gene3D; 3.90.230.10; -; 1.
DR HAMAP; MF_01974; MetAP_1; 1.
DR InterPro; IPR036005; Creatinase/aminopeptidase-like.
DR InterPro; IPR000994; Pept_M24.
DR InterPro; IPR001714; Pept_M24_MAP.
DR InterPro; IPR002467; Pept_M24A_MAP1.
DR InterPro; IPR031615; Zfn-C6H2.
DR Pfam; PF00557; Peptidase_M24; 1.
DR Pfam; PF15801; zf-C6H2; 1.
DR PRINTS; PR00599; MAPEPTIDASE.
DR SUPFAM; SSF55920; SSF55920; 1.
DR TIGRFAMs; TIGR00500; met_pdase_I; 1.
DR PROSITE; PS00680; MAP_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminopeptidase; Hydrolase; Metal-binding; Protease;
KW Reference proteome.
FT CHAIN 1..517
FT /note="Methionine aminopeptidase 1b"
FT /id="PRO_0000451190"
FT REGION 74..94
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 76..94
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 325
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174"
FT BINDING 342
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174"
FT BINDING 353
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174"
FT BINDING 353
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174,
FT ECO:0007744|PDB:3S6B"
FT BINDING 419
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174,
FT ECO:0007744|PDB:3S6B"
FT BINDING 426
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174"
FT BINDING 452
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174,
FT ECO:0007744|PDB:3S6B"
FT BINDING 483
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174"
FT BINDING 483
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_03174,
FT ECO:0007744|PDB:3S6B"
FT SITE 316
FT /note="Important for substrate specificity to methionine"
FT /evidence="ECO:0000269|PubMed:27023914"
FT MUTAGEN 316
FT /note="C->S: 50% reduction in activity with Zn(2+) as
FT cofactor. Increases activity with Co(2+) as cofactor and
FT acquires new substrate specificity to leucine, tryptophan
FT and phenylalanine."
FT /evidence="ECO:0000269|PubMed:27023914"
FT HELIX 173..180
FT /evidence="ECO:0007829|PDB:3S6B"
FT TURN 183..185
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 192..196
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 200..203
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 209..211
FT /evidence="ECO:0007829|PDB:3S6B"
FT TURN 231..235
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 239..242
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 255..277
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 285..298
FT /evidence="ECO:0007829|PDB:3S6B"
FT TURN 304..307
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 308..310
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 313..319
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 338..347
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 350..359
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 368..387
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 396..406
FT /evidence="ECO:0007829|PDB:3S6B"
FT TURN 407..409
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 418..420
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 422..431
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 433..436
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 448..451
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 454..458
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 462..464
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 471..473
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 479..481
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 483..489
FT /evidence="ECO:0007829|PDB:3S6B"
FT STRAND 492..495
FT /evidence="ECO:0007829|PDB:3S6B"
FT HELIX 512..514
FT /evidence="ECO:0007829|PDB:3S6B"
SQ SEQUENCE 517 AA; 59724 MW; BD216A8F8D25E7AF CRC64;
MANIDDIEKQ IENIKINSDD NKNNVSKNKN ILLNGVNLKD HEIKDNVKSV DYNNNNNEND
TMNEINKHVK NDEYCNKENS NNNNNNNNNN NNNLDTQINE TLNLNEKFEK KNEENLCSGC
KKVLIKKLSC PICLKNKIFS YFCNQECFKG SWKEHQKIHE NMNKENNEKE DHLKTIVKKH
LSPENFDPTN RKYWVYDDHL KNFVNFKFTG DVRPWPLSKI NHVPSHIERP DYAISSIPES
ELIYKRKSDI YVNNEEEIQR IREACILGRK TLDYAHTLVS PGVTTDEIDR KVHEFIIKNN
AYPSTLNYYK FPKSCCTSVN EIVCHGIPDY RPLKSGDIIN IDISVFYKGV HSDLNETYFV
GDINDVPKEG KELVETCYFS LMEAIKKCKP GMFYKNIGTL IDAYVSKKNF SVVRSYSGHG
VGKLFHSNPT VPHFKKNKAV GIMKPGHVFT IEPMINQGHY SDVLWPDQWT SATSDGKLSA
QFEHTLLITN NGVEILTKRT QDSPPLGFDT KDELYYN
