Carbamoyltransferase hypF - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P30131 (HYPF_ECOLI)

Last modified June 16, 2009. Version 85. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Carbamoyltransferase hypF
    EC=2.1.3.-
Alternative name(s):
    Carbamoyl phosphate-converting enzyme hypF
    [NiFe]-hydrogenase maturation factor hypF
      Short name=Hydrogenase maturation protein hypF

Gene names

Name:	hypF
Synonyms:	hydA
Ordered Locus Names:	b2712, JW5433

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	750 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Along with hypE, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of hypE yielding a protein-S-carboxamide. Ref.4 Ref.5 Ref.6 Ref.7
Pathway	Protein modification; [NiFe] hydrogenase maturation.
Subunit structure	Forms a complex with hypE.
Domain	Contains a version of the yrdC-like domain which probably has a different function than that of some proteins where it has been implicated in RNA binding. Contains a unique C-terminal domain with an O-carbamoyltransferase motif.
Sequence similarities	Belongs to the carbamoyltransferase hypF family. Contains 1 acylphosphatase-like domain. Contains 1 YrdC-like domain.

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Ontologies

Keywords
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Transferase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Molecular function	acylphosphatase activity Inferred from electronic annotation. Source: InterPro transcription regulator activity Inferred from electronic annotation. Source: InterPro transferase activity Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 750

750

Carbamoyltransferase hypF

PRO_0000071614

Regions

Domain

8 – 92

Acylphosphatase-like

Domain

200 – 376

177

YrdC-like

Zinc finger

109 – 134

C4-type Potential

Zinc finger

159 – 184

C4-type Potential

Region

19 – 23

Binds to substrate; phosphate group

Experimental info

Mutagenesis

R → E, H or K: Loss of activity. Ref.6

Mutagenesis

R → Q: Diminishes activity. Ref.6

Mutagenesis

112

C → A: Loss of activity.

Mutagenesis

162

C → A: Loss of activity.

Mutagenesis

475

H → A: Loss of activity.

Mutagenesis

476

H → A: Carbamoyl phosphate-dependent ATP hydrolysis activity diminished in vitro but sufficient for wild-type-like phenotype. Ref.6

Sequence conflict

31 – 32

QQ → RE in BAA03315. Ref.1

Sequence conflict

367 – 386

SGEML…LALPP → RRNAAPFAGVCAGCAGFAS in BAA03315. Ref.1

Sequence conflict

431 – 432

WR → CA in BAA03315. Ref.1

Sequence conflict

435

L → S in BAA03315. Ref.1

Secondary structure

750

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P30131-1 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 8BB245F80349A91E
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FASTA

750

82,066

        10         20         30         40         50         60 
MAKNTSCGVQ LRIRGKVQGV GFRPFVWQLA QQLNLHGDVC NDGDGVEVRL REDPETFLVQ 

        70         80         90        100        110        120 
LYQHCPPLAR IDSVEREPFI WSQLPTEFTI RQSTGGTMNT QIVPDAATCP ACLAEMNTPG 

       130        140        150        160        170        180 
ERRYRYPFIN CTHCGPRFTI IRAMPYDRPF TVMAAFPLCP ACDKEYRDPL DRRFHAQPVA 

       190        200        210        220        230        240 
CPECGPHLEW VSHGEHAEQE AALQAAIAQL KMGKIVAIKG IGGFHLACDA RNSNAVATLR 

       250        260        270        280        290        300 
ARKHRPAKPL AVMLPVADGL PDAARQLLTT PAAPIVLVDK KYVPELCDDI APDLNEVGVM 

       310        320        330        340        350        360 
LPANPLQHLL LQELQCPLVM TSGNLSGKPP AISNEQALAD LQGIADGFLI HNRDIVQRMD 

       370        380        390        400        410        420 
DSVVRESGEM LRRSRGYVPD ALALPPGFKN VPPVLCLGAD LKNTFCLVRG EQAVLSQHLG 

       430        440        450        460        470        480 
DLSDDGIQMQ WREALRLMQN IYDFTPQYVV HDAHPGYVSS QWAREMNLPT QTVLHHHAHA 

       490        500        510        520        530        540 
AACLAEHQWP LDGGDVIALT LDGIGMGENG ALWGGECLRV NYRECEHLGG LPAVALPGGD 

       550        560        570        580        590        600 
LAAKQPWRNL LAQCLRFVPE WQNYSETASV QQQNWSVLAR AIERGINAPL ASSCGRFFDA 

       610        620        630        640        650        660 
VAAALGCAPA TLSYEGEAAC ALEALAASCH GVTHPVTMPR VDNQLDLATF WQQWLNWQAP 

       670        680        690        700        710        720 
VNQRAWAFHD ALAQGFAALM REQATMRGIT TLVFSGGVIH NRLLRARLAH YLADFTLLFP 

       730        740        750 
QSLPAGDGGL SLGQGVIAAA RWLAGEVQNG

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References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence and functional analysis of hydA of E.coli." Tomiyama M., Shiotani M., Nishio M., Ikebukuro K., Sode K., Tamiya E., Karube I. Submitted (FEB-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Analysis of the hydA locus of Escherichia coli: two genes (hydN and hypF) involved in formate and hydrogen metabolism." Maier T., Binder U., Boeck A. Arch. Microbiol. 165:333-341(1996) [PubMed: 8661925] [Abstract] Cited for: FUNCTION.
[5]	"HypF, a carbamoyl phosphate-converting enzyme involved in [NiFe] hydrogenase maturation." Paschos A., Bauer A., Zimmermann A., Zehelein E., Boeck A. J. Biol. Chem. 277:49945-49951(2002) [PubMed: 12377778] [Abstract] Cited for: FUNCTION, MUTAGENESIS.
[6]	"Analysis of the transcarbamoylation-dehydration reaction catalyzed by the hydrogenase maturation proteins HypF and HypE." Blokesch M., Paschos A., Bauer A., Reissmann S., Drapal N., Boeck A. Eur. J. Biochem. 271:3428-3436(2004) [PubMed: 15291820] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF ARG-23 AND HIS-476.
[7]	"The complex between hydrogenase-maturation proteins HypC and HypD is an intermediate in the supply of cyanide to the active site iron of [NiFe]-hydrogenases." Blokesch M., Albracht S.P., Matzanke B.F., Drapal N.M., Jacobi A., Boeck A. J. Mol. Biol. 344:155-167(2004) [PubMed: 15504408] [Abstract] Cited for: FUNCTION.
[8]	"Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain." Rosano C., Zuccotti S., Bucciantini M., Stefani M., Ramponi G., Bolognesi M. J. Mol. Biol. 321:785-796(2002) [PubMed: 12206761] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.27 ANGSTROMS) OF 1-91 IN COMPLEX WITH SULFATE AND IN COMPLEX WITH SUBSTRATE.

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Cross-references

Sequence databases

D14422 Genomic DNA. Translation: BAA03315.1.
U29579 Genomic DNA. Translation: AAA69222.1.
U00096 Genomic DNA. Translation: AAC75754.1.
AP009048 Genomic DNA. Translation: BAE76789.1.

PIR

D65051.

RefSeq

AP_003279.1.
NP_417192.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GXT	X-ray	1.27	A	1-91	[»]
1GXU	X-ray	1.27	A	1-91	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10000N.

Genome annotation databases

GeneID

944963.

GenomeReviews

Gene locus JW5433 in contig AP009048_GR.
Gene locus b2712 in contig U00096_GR.

KEGG

ecj:JW5433.
eco:b2712.

Organism-specific databases

EchoBASE

EB1512.

EcoGene

EG11551. hypF.

CMR

Search...

Phylogenomic databases

HOGENOM

P30131.

OMA

P30131. HQHCPPL.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11551-MON.

Family and domain databases

InterPro

IPR001792. Acylphosphatase.
IPR017968. Acylphosphatase_CS.
IPR017945. DHBP_synth_RibB-like_a/b_dom.
IPR004421. Hyd_matr_HypF.
IPR006070. Sua5/yciO/yrdC_N.
IPR011125. Znf_HypF.
[Graphical view]

Gene3D

G3DSA:3.90.870.10. DHBP_synth_RibB-like_a/b_dom. 1 hit.

PANTHER

PTHR10029. Acylphosphatase. 1 hit.

Pfam

PF00708. Acylphosphatase. 1 hit.
PF01300. Sua5_yciO_yrdC. 1 hit.
PF07503. zf-HYPF. 2 hits.
[Graphical view]

PIRSF

PIRSF006256. CMPcnvr_hdrg_mat. 1 hit.

ProDom

PD001884. Acylphosphatase. 1 hit.
PD002209. SUA5/yciO/yrdC. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR00143. hypF. 1 hit.

PROSITE

PS00150. ACYLPHOSPHATASE_1. 1 hit.
PS00151. ACYLPHOSPHATASE_2. False negative.
PS51160. ACYLPHOSPHATASE_3. 1 hit.
PS51163. YRDC. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

HYPF_ECOLI

Accession

Primary (citable) accession number: P30131
Secondary accession number(s): Q2MAB7, Q46878

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	November 1, 1997
Last modified:	June 16, 2009
This is version 85 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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