NTR - protein - N(PI)-phosphohistidine/cysteine - sugar phosphotransferase activity

[gocentral]

NTR - protein - N(PI)-phosphohistidine/cysteine - sugar phosphotransferase activity.

Suggested definition: Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine/cysteine + N,N'-diacetylchitobiose(out) = protein histidine/cysteine + N,N'-diacetylchitobiose phosphate(in).

Child of GO:0008982. The source for the GO:0008982 term is EC 2.7.1.69 Protein EIIB N(pi)-phospho-L-histidine/cysteine + sugar <=> protein EIIB + sugar phosphate. In this reaction the phospho donor is specified as either a histidine or cysteine residue but there is no mention of phosphocysteines in the GO definition. Can the GO definition be modified so that phosphorylated cysteine residues which occur in GN PTS systems are covered explicitly.

Thanks Amanda

Reported by: amackie

Original Ticket: geneontology/ontology-requests/10736

[gocentral]

Sorry, that NTR request should have been for specifically for protein-N(PI)-phosphohistidine/cysteine - N,N'-diacetylchitobiose phosphotransferase system transporter activity.

Original comment by: amackie

[gocentral]

• labels: --> enzymes
• assigned_to: Tanya Berardini

Original comment by: tberardini

[gocentral]

Hi Amanda,

Can you give me a link for EC 2.7.1.69 that refers to the cysteine residue? I'm looking here: http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/1/69.html

I only see references to histidine and many of the exact synonyms of this GO term refer to histidine.

A PMID for a reference describing this activity would also be much appreciated.

I'll probably end up creating two terms:

protein-N(PI)-phosphohistidine - N,N'-diacetylchitobiose phosphotransferase system transporter activity.

and

protein-N(PI)-phosphocysteine - N,N'-diacetylchitobiose phosphotransferase system transporter activity

because each time this activity occurs, it will either transfer the phosphate from a phosphohistidine or a phosphocysteine but not from both at the same time.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

Hi Tanya,

I was looking at the Swiss Prot enzyme entry for EC2.7.1.69. The link is http://enzyme.expasy.org/EC/2.7.1.69.

Regarding PMIDs, 8246840 (Postma 1993) is a comprehensive review of bacterial PTS while 10913119 (Keyhani 2000) contains a specific desccription of the phosphotransfer reactions in the E. coli chitobiose PTS.

I did think about requesting a new term to cover phosphotransfer from a cysteine residue but then hesitated when I saw the Swiss Prot definition.

Amanda

Original comment by: amackie

[gocentral]

Here's my plan:

(1) NEW1: protein-N(PI)-phosphohistidine - N,N'-diacetylchitobiose phosphotransferase system transporter activity is_a protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, GO:0008982 PMID:10913119

(2) NEW2: protein-N(PI)-phosphocysteine - N,N'-diacetylchitobiose phosphotransferase system transporter activity is_a phosphotransferase activity, alcohol group as acceptor, GO:0016773 is_a active transmembrane transporter activity, GO:0022804 is_a carbohydrate transmembrane transporter activity, GO:0015144 PMID:10913119

What do you think?

Original comment by: tberardini

[gocentral]

Hi Tanya,

I'm by no means an expert in GO but looking at this I wondered whether your NEW2 term should have parent term (also new) of protein-N(PI)-phosphocysteine-sugar phosphotransferase activity eg NEW2: protein-N(PI)-phosphocysteine - N,N'-diacetylchitobiose phosphotransferase system transporter activity is a NEW3: protein-N(PI)-phosphocysteine-sugar phosphotransferase activity is_a phosphotransferase activity, alcohol group as acceptor, GO:0016773 is_a active transmembrane transporter activity, GO:0022804 is_a carbohydrate transmembrane transporter activity, GO:0015144

I'll leave it up to you - both ways would work for my purposes

Amanda

On 5/04/2014 11:26 AM, Tanya Berardini wrote:

Here's my plan:

(1) NEW1: protein-N(PI)-phosphohistidine - N,N'-diacetylchitobiose phosphotransferase system transporter activity is_a protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, GO:0008982 PMID:10913119

(2) NEW2: protein-N(PI)-phosphocysteine - N,N'-diacetylchitobiose phosphotransferase system transporter activity is_a phosphotransferase activity, alcohol group as acceptor, GO:0016773 is_a active transmembrane transporter activity, GO:0022804 is_a carbohydrate transmembrane transporter activity, GO:0015144 PMID:10913119

What do you think?

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[ontology-requests:#10736] http://sourceforge.net/p/geneontology/ontology-requests/10736/ NTR - protein - N(PI)-phosphohistidine/cysteine - sugar phosphotransferase activity

Status: open Group: None Labels: enzymes Created: Wed Mar 26, 2014 03:01 AM UTC by Amanda Mackie Last Updated: Fri Mar 28, 2014 10:58 PM UTC Owner: Tanya Berardini

NTR - protein - N(PI)-phosphohistidine/cysteine - sugar phosphotransferase activity.

Suggested definition: Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine/cysteine + N,N'-diacetylchitobiose(out) = protein histidine/cysteine + N,N'-diacetylchitobiose phosphate(in).

Child of GO:0008982. The source for the GO:0008982 term is EC 2.7.1.69 Protein EIIB N(pi)-phospho-L-histidine/cysteine + sugar <=> protein EIIB + sugar phosphate. In this reaction the phospho donor is specified as either a histidine or cysteine residue but there is no mention of phosphocysteines in the GO definition. Can the GO definition be modified so that phosphorylated cysteine residues which occur in GN PTS systems are covered explicitly.

Thanks Amanda

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Original comment by: amackie

[gocentral]

Been thinking and reading about this some more Tanya and I have a couple of things to add.

Firstly the definitions for the phosphocysteine related terms should use the phrase protein-phosphocysteine (or perhaps protein-S-phosphocysteine). No need for N(pi) which I think refers to the specific N atom in histidine that is phosphorylated. Sorry - should have picked that up earlier.

Secondly, in many of the E. coli PTS systems the final phosphotransfer is from a phosphocysteine residue in the EIIB domain of the transporter to the incoming sugar. If you do decide that separate terms are needed for phosphocysteine donors and phosphohistidine donors then I will need to request new terms for a few of these transporters

So for example I will need new terms for protein-phosphocysteine-glucose phosphotransferase system transporter activity, protein-phosphocysteine-mannitol phosphotransferase system transporter activity and others

If this is the case then there should definitely be a new generic term for protein-phosphocysteine-sugar phosphotransferase activity

Hope that all makes sense

Amanda

Original comment by: amackie

[gocentral]

Yes, I think we should definitely split the phospho-his and phospho-cys activities.

So for example I will need new terms for protein-phosphocysteine-glucose phosphotransferase system transporter activity, protein-phosphocysteine-mannitol phosphotransferase system transporter activity and >others

Ok. Which ones should we start with? Just these two?

If this is the case then there should definitely be a new generic term for protein-phosphocysteine-sugar phosphotransferase activity

Agreed.

Original comment by: tberardini

[gocentral]

Added these four terms:

[Term] +id: GO:0090562 +name: protein-N(PI)-phosphohistidine - N,N'-diacetylchitobiose phosphotransferase system transporter activity +namespace: molecular_function +def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + N,N'-diacetylchitobiose(out) = protein histidine + N,N'-diacetylchitobiose phosphate(in)." [PMID:10913119] +is_a: GO:0008982 ! protein-N(PI)-phosphohistidine-sugar phosphotransferase activity

+[Term] +id: GO:0090563 +name: protein-phosphocysteine-sugar phosphotransferase activity +namespace: molecular_function +def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphocysteine + sugar(out) = protein cysteine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:am] +is_a: GO:0015144 ! carbohydrate transmembrane transporter activity +is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor +is_a: GO:0022804 ! active transmembrane transporter activity

+[Term] +id: GO:0090564 +name: protein-phosphocysteine-glucose phosphotransferase system transporter activity +namespace: molecular_function +def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphocysteine + glucose(out) = protein cysteine + glucose phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:am] +is_a: GO:0090563 ! protein-phosphocysteine-sugar phosphotransferase activity

+[Term] +id: GO:0090565 +name: protein-phosphocysteine-mannitol phosphotransferase system transporter activity +namespace: molecular_function +def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphocysteine + mannitol(out) = protein cysteine + mannitol phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport." [GOC:am] +is_a: GO:0090563 ! protein-phosphocysteine-sugar phosphotransferase activity

Please check definitions and parentage to make sure that I captured our discussion correctly.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

One more:

[Term] +id: GO:0090566 +name: protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity +namespace: molecular_function +def: "Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphocysteine + N,N'-diacetylchitobiose(out) = protein cysteine + N,N'-diacetylchitobiose phosphate(in)." [GOC:am, PMID:10913119] +is_a: GO:0090563 ! protein-phosphocysteine-sugar phosphotransferase activity

Original comment by: tberardini

[gocentral]

• status: open --> closed-accepted

Original comment by: tberardini

[gocentral]

Thanks for the new terms. In all the defs the term 'protein N-phosphocysteine' should be replaced by protein S-phosphocysteine'

Amanda

Original comment by: amackie

[gocentral]

Good catch! Done. N-phosphocysteine -> S-phosphocysteine

Thanks.

Original comment by: tberardini