HYPF_ECOLI
ID HYPF_ECOLI Reviewed; 750 AA.
AC P30131; Q2MAB7; Q46878;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Carbamoyltransferase HypF {ECO:0000305};
DE EC=6.2.-.- {ECO:0000269|PubMed:12586941, ECO:0000269|PubMed:15291820};
DE AltName: Full=Carbamoyl phosphate-converting enzyme HypF;
DE AltName: Full=[NiFe]-hydrogenase maturation factor HypF;
DE Short=Hydrogenase maturation protein HypF;
GN Name=hypF {ECO:0000303|PubMed:8661925}; Synonyms=hydA {ECO:0000303|Ref.1};
GN OrderedLocusNames=b2712, JW5433;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RA Tomiyama M., Shiotani M., Nishio M., Ikebukuro K., Sode K., Tamiya E.,
RA Karube I.;
RT "Nucleotide sequence and functional analysis of hydA of E.coli.";
RL Submitted (FEB-1993) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=8661925; DOI=10.1007/s002030050335;
RA Maier T., Binder U., Boeck A.;
RT "Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF)
RT involved in formate and hydrogen metabolism.";
RL Arch. Microbiol. 165:333-341(1996).
RN [5]
RP FUNCTION, SUBUNIT, AND MUTAGENESIS OF ARG-23; CYS-109; CYS-159; HIS-475;
RP HIS-476 AND HIS-479.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=12377778; DOI=10.1074/jbc.m204601200;
RA Paschos A., Bauer A., Zimmermann A., Zehelein E., Boeck A.;
RT "HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe]
RT hydrogenase maturation.";
RL J. Biol. Chem. 277:49945-49951(2002).
RN [6]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=12586941; DOI=10.1126/science.1080972;
RA Reissmann S., Hochleitner E., Wang H., Paschos A., Lottspeich F.,
RA Glass R.S., Boeck A.;
RT "Taming of a poison: biosynthesis of the NiFe-hydrogenase cyanide
RT ligands.";
RL Science 299:1067-1070(2003).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH HYPE, AND MUTAGENESIS OF
RP ARG-23 AND HIS-476.
RX PubMed=15291820; DOI=10.1111/j.1432-1033.2004.04280.x;
RA Blokesch M., Paschos A., Bauer A., Reissmann S., Drapal N., Boeck A.;
RT "Analysis of the transcarbamoylation-dehydration reaction catalyzed by the
RT hydrogenase maturation proteins HypF and HypE.";
RL Eur. J. Biochem. 271:3428-3436(2004).
RN [8]
RP INTERACTION WITH HYPE.
RX PubMed=18065529; DOI=10.1128/jb.01610-07;
RA Rangarajan E.S., Asinas A., Proteau A., Munger C., Baardsnes J.,
RA Iannuzzi P., Matte A., Cygler M.;
RT "Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia
RT coli and its interaction with HypF.";
RL J. Bacteriol. 190:1447-1458(2008).
RN [9] {ECO:0007744|PDB:1GXT, ECO:0007744|PDB:1GXU}
RP X-RAY CRYSTALLOGRAPHY (1.27 ANGSTROMS) OF 1-91 IN COMPLEXES WITH SUBSTRATE
RP ANALOGS.
RX PubMed=12206761; DOI=10.1016/s0022-2836(02)00713-1;
RA Rosano C., Zuccotti S., Bucciantini M., Stefani M., Ramponi G.,
RA Bolognesi M.;
RT "Crystal structure and anion binding in the prokaryotic hydrogenase
RT maturation factor HypF acylphosphatase-like domain.";
RL J. Mol. Biol. 321:785-796(2002).
CC -!- FUNCTION: Involved in the maturation of [NiFe] hydrogenases
CC (PubMed:8661925, PubMed:12377778, PubMed:12586941). Along with HypE, it
CC catalyzes the synthesis of the CN ligands of the active site iron of
CC [NiFe]-hydrogenases (PubMed:12586941). HypF functions as a carbamoyl
CC transferase using carbamoylphosphate as a substrate and transferring
CC the carboxamido moiety in an ATP-dependent reaction to the thiolate of
CC the C-terminal cysteine of HypE yielding a protein-S-carboxamide
CC (PubMed:12586941, PubMed:15291820). In the absence of any other
CC substrate, displays carbamoyl-phosphate phosphatase activity
CC (PubMed:12377778). {ECO:0000269|PubMed:12377778,
CC ECO:0000269|PubMed:12586941, ECO:0000269|PubMed:15291820,
CC ECO:0000269|PubMed:8661925}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + C-terminal L-cysteinyl-[HypE protein] + carbamoyl
CC phosphate + H2O = AMP + C-terminal S-carboxamide-L-cysteinyl-[HypE
CC protein] + diphosphate + H(+) + phosphate; Xref=Rhea:RHEA:55636,
CC Rhea:RHEA-COMP:14247, Rhea:RHEA-COMP:14392, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58228, ChEBI:CHEBI:76913,
CC ChEBI:CHEBI:139126, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:12586941, ECO:0000269|PubMed:15291820};
CC -!- PATHWAY: Protein modification; [NiFe] hydrogenase maturation.
CC {ECO:0000305}.
CC -!- SUBUNIT: Monomer (PubMed:12377778). Forms a complex with HypE
CC (PubMed:15291820, PubMed:18065529). {ECO:0000269|PubMed:12377778,
CC ECO:0000269|PubMed:15291820, ECO:0000269|PubMed:18065529}.
CC -!- INTERACTION:
CC P30131; P24193: hypE; NbExp=2; IntAct=EBI-9128507, EBI-552743;
CC -!- DOMAIN: Contains a version of the YrdC-like domain which probably has a
CC different function than that of some proteins where it has been
CC implicated in RNA binding.
CC -!- DOMAIN: Contains a unique C-terminal domain with an O-
CC carbamoyltransferase motif.
CC -!- DISRUPTION PHENOTYPE: Deletion of the gene results in the loss of
CC hydrogenase activity and in the synthesis of the large subunits of the
CC hydrogenase 1, 2 and 3 in the inactive precursor form.
CC {ECO:0000269|PubMed:8661925}.
CC -!- SIMILARITY: Belongs to the carbamoyltransferase HypF family.
CC {ECO:0000305}.
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DR EMBL; D14422; BAA03315.1; -; Genomic_DNA.
DR EMBL; U29579; AAA69222.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75754.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76789.1; -; Genomic_DNA.
DR PIR; D65051; D65051.
DR RefSeq; NP_417192.1; NC_000913.3.
DR RefSeq; WP_001107704.1; NZ_LN832404.1.
DR PDB; 1GXT; X-ray; 1.30 A; A=1-91.
DR PDB; 1GXU; X-ray; 1.27 A; A=1-91.
DR PDBsum; 1GXT; -.
DR PDBsum; 1GXU; -.
DR AlphaFoldDB; P30131; -.
DR SMR; P30131; -.
DR BioGRID; 4259427; 14.
DR BioGRID; 849360; 8.
DR ComplexPortal; CPX-5281; HypEF Ni-hydrogenase maturation complex.
DR DIP; DIP-10000N; -.
DR IntAct; P30131; 8.
DR STRING; 511145.b2712; -.
DR jPOST; P30131; -.
DR PaxDb; P30131; -.
DR PRIDE; P30131; -.
DR EnsemblBacteria; AAC75754; AAC75754; b2712.
DR EnsemblBacteria; BAE76789; BAE76789; BAE76789.
DR GeneID; 944963; -.
DR KEGG; ecj:JW5433; -.
DR KEGG; eco:b2712; -.
DR PATRIC; fig|1411691.4.peg.4030; -.
DR EchoBASE; EB1512; -.
DR eggNOG; COG0068; Bacteria.
DR HOGENOM; CLU_009164_0_0_6; -.
DR InParanoid; P30131; -.
DR OMA; VQHHYAH; -.
DR PhylomeDB; P30131; -.
DR BioCyc; EcoCyc:EG11551-MON; -.
DR BioCyc; MetaCyc:EG11551-MON; -.
DR UniPathway; UPA00335; -.
DR EvolutionaryTrace; P30131; -.
DR PRO; PR:P30131; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:1904949; C:ATPase complex; IPI:ComplexPortal.
DR GO; GO:0016743; F:carboxyl- or carbamoyltransferase activity; IDA:EcoCyc.
DR GO; GO:0003725; F:double-stranded RNA binding; IEA:InterPro.
DR GO; GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0046892; P:peptidyl-S-carbamoyl-L-cysteine dehydration; IDA:ComplexPortal.
DR GO; GO:0046944; P:protein carbamoylation; IDA:EcoCyc.
DR GO; GO:0051604; P:protein maturation; IDA:EcoCyc.
DR InterPro; IPR001792; Acylphosphatase-like_dom.
DR InterPro; IPR036046; Acylphosphatase-like_dom_sf.
DR InterPro; IPR017968; Acylphosphatase_CS.
DR InterPro; IPR004421; Carbamoyltransferase_HypF.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR041440; HypF_C.
DR InterPro; IPR006070; YrdC-like_dom.
DR InterPro; IPR011125; Znf_HypF.
DR Pfam; PF00708; Acylphosphatase; 1.
DR Pfam; PF17788; HypF_C; 1.
DR Pfam; PF01300; Sua5_yciO_yrdC; 1.
DR Pfam; PF07503; zf-HYPF; 2.
DR PIRSF; PIRSF006256; CMPcnvr_hdrg_mat; 1.
DR SUPFAM; SSF54975; SSF54975; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00143; hypF; 1.
DR PROSITE; PS00150; ACYLPHOSPHATASE_1; 1.
DR PROSITE; PS51160; ACYLPHOSPHATASE_3; 1.
DR PROSITE; PS51163; YRDC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Ligase; Metal-binding; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..750
FT /note="Carbamoyltransferase HypF"
FT /id="PRO_0000071614"
FT DOMAIN 8..92
FT /note="Acylphosphatase-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00520"
FT DOMAIN 200..376
FT /note="YrdC-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00518"
FT ZN_FING 109..134
FT /note="C4-type"
FT /evidence="ECO:0000305|PubMed:12377778"
FT ZN_FING 159..184
FT /note="C4-type"
FT /evidence="ECO:0000305|PubMed:12377778"
FT BINDING 19..23
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:12206761"
FT MUTAGEN 23
FT /note="R->E,H: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12377778,
FT ECO:0000269|PubMed:15291820"
FT MUTAGEN 23
FT /note="R->Q: Diminishes activity."
FT /evidence="ECO:0000269|PubMed:12377778,
FT ECO:0000269|PubMed:15291820"
FT MUTAGEN 109
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12377778"
FT MUTAGEN 159
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:12377778"
FT MUTAGEN 475
FT /note="H->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:12377778"
FT MUTAGEN 476
FT /note="H->A: Carbamoyl phosphate-dependent ATP hydrolysis
FT activity diminished in vitro but sufficient for wild-type-
FT like phenotype."
FT /evidence="ECO:0000269|PubMed:12377778,
FT ECO:0000269|PubMed:15291820"
FT MUTAGEN 479
FT /note="H->A: No change in activity."
FT /evidence="ECO:0000269|PubMed:12377778"
FT CONFLICT 31..32
FT /note="QQ -> RE (in Ref. 1; BAA03315)"
FT /evidence="ECO:0000305"
FT CONFLICT 367..386
FT /note="SGEMLRRSRGYVPDALALPP -> RRNAAPFAGVCAGCAGFAS (in Ref.
FT 1; BAA03315)"
FT /evidence="ECO:0000305"
FT CONFLICT 431..432
FT /note="WR -> CA (in Ref. 1; BAA03315)"
FT /evidence="ECO:0000305"
FT CONFLICT 435
FT /note="L -> S (in Ref. 1; BAA03315)"
FT /evidence="ECO:0000305"
FT STRAND 6..16
FT /evidence="ECO:0007829|PDB:1GXT"
FT STRAND 18..21
FT /evidence="ECO:0007829|PDB:1GXT"
FT HELIX 22..33
FT /evidence="ECO:0007829|PDB:1GXT"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:1GXT"
FT STRAND 43..52
FT /evidence="ECO:0007829|PDB:1GXT"
FT HELIX 55..63
FT /evidence="ECO:0007829|PDB:1GXT"
FT STRAND 70..83
FT /evidence="ECO:0007829|PDB:1GXT"
FT STRAND 86..90
FT /evidence="ECO:0007829|PDB:1GXT"
SQ SEQUENCE 750 AA; 82066 MW; 8BB245F80349A91E CRC64;
MAKNTSCGVQ LRIRGKVQGV GFRPFVWQLA QQLNLHGDVC NDGDGVEVRL REDPETFLVQ
LYQHCPPLAR IDSVEREPFI WSQLPTEFTI RQSTGGTMNT QIVPDAATCP ACLAEMNTPG
ERRYRYPFIN CTHCGPRFTI IRAMPYDRPF TVMAAFPLCP ACDKEYRDPL DRRFHAQPVA
CPECGPHLEW VSHGEHAEQE AALQAAIAQL KMGKIVAIKG IGGFHLACDA RNSNAVATLR
ARKHRPAKPL AVMLPVADGL PDAARQLLTT PAAPIVLVDK KYVPELCDDI APDLNEVGVM
LPANPLQHLL LQELQCPLVM TSGNLSGKPP AISNEQALAD LQGIADGFLI HNRDIVQRMD
DSVVRESGEM LRRSRGYVPD ALALPPGFKN VPPVLCLGAD LKNTFCLVRG EQAVLSQHLG
DLSDDGIQMQ WREALRLMQN IYDFTPQYVV HDAHPGYVSS QWAREMNLPT QTVLHHHAHA
AACLAEHQWP LDGGDVIALT LDGIGMGENG ALWGGECLRV NYRECEHLGG LPAVALPGGD
LAAKQPWRNL LAQCLRFVPE WQNYSETASV QQQNWSVLAR AIERGINAPL ASSCGRFFDA
VAAALGCAPA TLSYEGEAAC ALEALAASCH GVTHPVTMPR VDNQLDLATF WQQWLNWQAP
VNQRAWAFHD ALAQGFAALM REQATMRGIT TLVFSGGVIH NRLLRARLAH YLADFTLLFP
QSLPAGDGGL SLGQGVIAAA RWLAGEVQNG
