HYPD_CLODI
ID HYPD_CLODI Reviewed; 789 AA.
AC A0A031WDE4;
DT 12-SEP-2018, integrated into UniProtKB/Swiss-Prot.
DT 09-JUL-2014, sequence version 1.
DT 25-MAY-2022, entry version 43.
DE RecName: Full=Trans-4-hydroxy-L-proline dehydratase {ECO:0000303|PubMed:28183913};
DE EC=4.2.1.172 {ECO:0000269|PubMed:28183913};
DE AltName: Full=Glycyl radical enzyme {ECO:0000305};
DE AltName: Full=Hyp dehydratase {ECO:0000303|PubMed:28183913};
GN Name=pflD {ECO:0000303|Ref.1};
GN Synonyms=csdB_2 {ECO:0000312|EMBL:SJT80202.1};
GN ORFNames=BGU81_07860 {ECO:0000312|EMBL:PBG28510.1},
GN BN1095_640054 {ECO:0000312|EMBL:CDT68933.1},
GN BN1096_740112 {ECO:0000312|EMBL:CDS89454.1},
GN BN1097_360077 {ECO:0000312|EMBL:CDS85123.1},
GN SAMEA3375004_02654 {ECO:0000312|EMBL:SJT80202.1};
OS Clostridioides difficile (Peptoclostridium difficile).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Clostridioides.
OX NCBI_TaxID=1496;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=7032989 {ECO:0000312|EMBL:CDT68933.1}, and
RC 7032994 {ECO:0000312|EMBL:CDS85123.1};
RA Monot M.;
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=6636-R/ST48 {ECO:0000312|EMBL:PBG28510.1};
RA Kociolek L.K., Ozer E.A.;
RT "Genomic characterization of C. difficile isolates from children.";
RL Submitted (NOV-2016) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VRECD0033 {ECO:0000312|EMBL:SJT80202.1};
RG Pathogen Informatics;
RL Submitted (FEB-2017) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND GLYCYL
RP RADICAL AT GLY-765.
RC STRAIN=70-100-2010;
RX PubMed=28183913; DOI=10.1126/science.aai8386;
RA Levin B.J., Huang Y.Y., Peck S.C., Wei Y., Martinez-Del Campo A.,
RA Marks J.A., Franzosa E.A., Huttenhower C., Balskus E.P.;
RT "A prominent glycyl radical enzyme in human gut microbiomes metabolizes
RT trans-4-hydroxy-L-proline.";
RL Science 355:1-28(2017).
CC -!- FUNCTION: Glycine radical enzyme that catalyzes the dehydration of the
CC non-proteinogenic amino acid trans-4-hydroxy-L-proline (Hyp) to produce
CC delta(1)-pyrroline-5-carboxylate (P5C). Is involved in the anaerobic
CC degradation of 4-hydroxyproline. {ECO:0000269|PubMed:28183913}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=trans-4-hydroxy-L-proline = (S)-1-pyrroline-5-carboxylate +
CC H(+) + H2O; Xref=Rhea:RHEA:54644, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:17388, ChEBI:CHEBI:58375;
CC EC=4.2.1.172; Evidence={ECO:0000269|PubMed:28183913};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.2 mM for trans-4-hydroxy-L-proline
CC {ECO:0000269|PubMed:28183913};
CC Note=kcat is 45 sec(-1) for trans-4-hydroxy-L-proline as substrate.
CC {ECO:0000269|PubMed:28183913};
CC -!- PTM: Requires the activating protein PflE to generate the key active
CC site glycyl radical on Gly-765 that is involved in catalysis.
CC {ECO:0000269|PubMed:28183913}.
CC -!- SIMILARITY: Belongs to the glycyl radical enzyme (GRE) family. HYPD
CC subfamily. {ECO:0000305}.
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DR EMBL; LK932372; CDS85123.1; -; Genomic_DNA.
DR EMBL; LK932529; CDS89454.1; -; Genomic_DNA.
DR EMBL; LK933338; CDT68933.1; -; Genomic_DNA.
DR EMBL; MPEQ01000010; PBG28510.1; -; Genomic_DNA.
DR EMBL; FURH01000003; SJT80202.1; -; Genomic_DNA.
DR RefSeq; WP_021363977.1; NZ_VINA01000003.1.
DR PDB; 6VXC; X-ray; 2.05 A; A/B/C/D/E/F/G/H=1-789.
DR PDB; 6VXE; X-ray; 2.46 A; A/B/C/D/E/F/G/H=1-789.
DR PDBsum; 6VXC; -.
DR PDBsum; 6VXE; -.
DR AlphaFoldDB; A0A031WDE4; -.
DR SMR; A0A031WDE4; -.
DR EnsemblBacteria; PBG28510; PBG28510; BGU81_07860.
DR GeneID; 66355776; -.
DR GO; GO:0016835; F:carbon-oxygen lyase activity; IDA:UniProtKB.
DR GO; GO:0019492; P:proline salvage; IDA:UniProtKB.
DR InterPro; IPR001150; Gly_radical.
DR InterPro; IPR004184; PFL_dom.
DR Pfam; PF01228; Gly_radical; 1.
DR Pfam; PF02901; PFL-like; 1.
DR PROSITE; PS51149; GLY_RADICAL_2; 1.
DR PROSITE; PS51554; PFL; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Organic radical.
FT CHAIN 1..789
FT /note="Trans-4-hydroxy-L-proline dehydratase"
FT /id="PRO_0000445027"
FT DOMAIN 7..663
FT /note="PFL"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00887"
FT DOMAIN 670..789
FT /note="Glycine radical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00493"
FT ACT_SITE 434
FT /note="Cysteine radical intermediate"
FT /evidence="ECO:0000250|UniProtKB:Q30W70"
FT ACT_SITE 436
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q30W70"
FT MOD_RES 765
FT /note="Glycine radical"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00493,
FT ECO:0000269|PubMed:28183913"
FT HELIX 7..18
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 26..38
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 39..41
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 44..58
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 91..99
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 109..117
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 119..123
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 124..126
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 128..135
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 138..145
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 152..155
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 166..169
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 172..185
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 188..190
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 194..228
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 232..247
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 248..250
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 256..273
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 285..298
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 304..319
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 328..333
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 342..348
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 358..370
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 373..381
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 387..397
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 406..408
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 409..418
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 423..426
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 430..432
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 433..435
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 436..438
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 442..452
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 453..461
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 462..464
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 467..470
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 480..482
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 486..518
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 522..527
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 531..534
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 538..540
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 543..553
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 555..568
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 569..571
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 577..585
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 586..590
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 592..600
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 610..627
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 637..642
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 647..653
FT /evidence="ECO:0007829|PDB:6VXE"
FT TURN 676..678
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 683..691
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 695..697
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 704..707
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 709..712
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 714..730
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 735..739
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 743..751
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 753..755
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 760..762
FT /evidence="ECO:0007829|PDB:6VXE"
FT STRAND 764..769
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 770..772
FT /evidence="ECO:0007829|PDB:6VXE"
FT HELIX 775..782
FT /evidence="ECO:0007829|PDB:6VXE"
SQ SEQUENCE 789 AA; 89175 MW; 9CC72891AE3505E5 CRC64;
MARGTFERTK KLREESINAE PHISIERAVL MTEAYKKYEG SVEIPVLRAL SFKHYIENRT
LSINDGELIV GEKGDSPNGA PTYPEICCHT MEDLEVMHNR DIINFSVSEE ARKIHKEEII
PFWKKRQTRD KIINAMTPEW LAAYEAGMFT EFMEQRAPGH TVCGDTIYKK GFLDLKKDIE
ARLKELDFLN DLDAYNKKAD LEAMAIACDA MVILGKRYAE KARQMAEEET DEAKKKDLLL
IAETCDVVPA HKPETYHQAI QMYWFVHIGV TTELNIWDAF TPGRLDQHLN PFYERDVENG
ILDRDRAQEL LECLWVKFNN QPAPPKVGIT LKESSTYTDF ANINTGGINP DGQDGVNEVS
YIILDVMDEM KLIQPSSNVQ ISKKTPQKFL KRACEISRKG WGQPAFYNTE AIVQELMEAG
KTIEDARLGG TSGCVETGCF GKEAYVLTGY MNIPKILELT LNNGYDPISK KQIGIETGDP
RNFQSYEELF EAFKKQLHYM IDIKIEGNAV IENICAKHMP CPLMSTIVDD CIEKGKDYQR
GGARYNTRYI QGVGIGTITD SLTAIKYNVF DKKKFDMDTL LKALDANFEG YEAILNLVSN
KTPKYGNDDD YADEIMQEIF NAYYNEVTGR PTVCGGEYRV DMLPTTCHIY FGEIMGASPN
GRLCAKPVSE GISPEKGGDT NGPTAVIKSC AKMDHIKTGG TLLNQRFAPS VVQGEKGLDN
MANLVRAYFN MDGHHIQFNV FDKNVLLEAQ KNPQDYKDLI VRVAGYSDHF NNLSRTLQDE
IIGRTEQTF
