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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   FIC PROTEIN FROM NEISSERIA MENINGITIDIS MUTANT DELTA8 IN COMPLEX WITH AMPPNP

Authors :   A. Goepfert, F. Stanger, T. Schirmer

Date :   10 Jun 11 (Deposition) - 25 Jan 12 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Ampylation, Adenylylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Engel, A. Goepfert, F. V. Stanger, A. Harms, A. Schmidt, T. Schirmer C. Dehio
Adenylylation Control By Intra- Or Intermolecular Active-Site Obstruction In Fic Proteins.
Nature V. 482 107 2012
PubMed-ID: 22266942 | Reference-DOI: 10.1038/NATURE10729

Molecule 1 - CELL FILAMENTATION PROTEIN FIC-RELATED PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSFDUET1
	Expression System Strain	:	BL21 AI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NMB0255
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	491
	Strain	:	SEROGROUP B

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ANP	4	Ligand/Ion	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	P6G	4	Ligand/Ion	HEXAETHYLENE GLYCOL

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:67 , ASN A:104 , HIS A:107 , GLY A:112 , ASN A:113 , GLY A:114 , ARG A:115 , ARG A:118 , LYS A:140 , TYR A:143 , LEU A:144 , MET A:147 , GLU A:148 , MG A:203 , HOH A:325 , HOH A:332 , HOH A:372 , HOH A:390 , HOH A:391 , HOH A:410	BINDING SITE FOR RESIDUE ANP A 201
02	AC2	SOFTWARE	ASP A:30 , ARG A:33 , TYR A:48 , HOH A:394	BINDING SITE FOR RESIDUE P6G A 202
03	AC3	SOFTWARE	ANP A:201 , HOH A:390 , HOH A:410	BINDING SITE FOR RESIDUE MG A 203
04	AC4	SOFTWARE	LYS B:67 , PHE B:72 , ASN B:104 , HIS B:107 , GLY B:112 , ASN B:113 , GLY B:114 , ARG B:115 , ARG B:118 , LYS B:140 , TYR B:143 , LEU B:144 , MET B:147 , GLU B:148 , MG B:204 , HOH B:348 , HOH B:371 , HOH B:392 , HOH B:393 , HOH B:394	BINDING SITE FOR RESIDUE ANP B 201
05	AC5	SOFTWARE	HOH B:382 , LYS C:126 , LYS C:130 , VAL C:132 , ASP C:167	BINDING SITE FOR RESIDUE P6G B 202
06	AC6	SOFTWARE	LYS B:131 , LEU B:165 , SER C:28	BINDING SITE FOR RESIDUE P6G B 203
07	AC7	SOFTWARE	ANP B:201 , HOH B:393 , HOH B:394	BINDING SITE FOR RESIDUE MG B 204
08	AC8	SOFTWARE	LYS C:67 , ASN C:104 , HIS C:107 , GLU C:111 , GLY C:112 , ASN C:113 , GLY C:114 , ARG C:115 , ARG C:118 , LYS C:140 , TYR C:143 , LEU C:144 , MET C:147 , GLU C:148 , MG C:203 , HOH C:314 , HOH C:364 , HOH C:381 , HOH C:420	BINDING SITE FOR RESIDUE ANP C 201
09	AC9	SOFTWARE	ARG C:24 , TYR C:48 , GLY C:51 , ASP C:55 , HOH C:356 , HOH C:384	BINDING SITE FOR RESIDUE P6G C 202
10	BC1	SOFTWARE	ANP C:201 , HOH C:420 , HOH C:421	BINDING SITE FOR RESIDUE MG C 203
11	BC2	SOFTWARE	LYS D:67 , ASN D:104 , HIS D:107 , GLY D:112 , ASN D:113 , GLY D:114 , ARG D:115 , ARG D:118 , LYS D:140 , TYR D:143 , LEU D:144 , MET D:147 , GLU D:148 , MG D:202 , HOH D:360 , HOH D:373 , HOH D:385 , HOH D:399	BINDING SITE FOR RESIDUE ANP D 201
12	BC3	SOFTWARE	ANP D:201 , HOH D:377 , HOH D:399	BINDING SITE FOR RESIDUE MG D 202

(no "SS Bond" information available for 3SE5)

(no "Cis Peptide Bond" information available for 3SE5)

(no "SAP(SNP)/Variant" information available for 3SE5)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIDO	PS51459	Fido domain profile.	NMFIC_NEIMB	37-162	4	A:37-162 B:37-162 C:37-162 D:37-162

(no "Exon" information available for 3SE5)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:155
 aligned with NMFIC_NEIMB | Q7DDR9 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:155
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
          NMFIC_NEIMB    13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..............ee..ee.....hhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhh...hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------FIDO  PDB: A:37-162 UniProt: 37-162                                                                                           ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3se5 A  13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with NMFIC_NEIMB | Q7DDR9 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:155
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
          NMFIC_NEIMB    13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..............ee..ee..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhh...hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------FIDO  PDB: B:37-162 UniProt: 37-162                                                                                           ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3se5 B  13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with NMFIC_NEIMB | Q7DDR9 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:155
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
          NMFIC_NEIMB    13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..............ee..ee.....hhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhh...hhhhhhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------FIDO  PDB: C:37-162 UniProt: 37-162                                                                                           ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3se5 C  13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain D from PDB  Type:PROTEIN  Length:155
 aligned with NMFIC_NEIMB | Q7DDR9 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:155
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
          NMFIC_NEIMB    13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..............ee..ee.....hhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.ee.hhhhhhhhhhhhhhhh...hhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------FIDO  PDB: D:37-162 UniProt: 37-162                                                                                           ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3se5 D  13 SIDEQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANAMYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNWQNVSKTLYLQAMERSPVNDLELRFLLKDNLTD 167
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3SE5)

(no "CATH Domain" information available for 3SE5)

(no "Pfam Domain" information available for 3SE5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (NMFIC_NEIMB | Q7DDR9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0070733	protein adenylyltransferase activity	Catalysis of the reaction: ATP + protein = diphosphate + adenylyl-protein; mediates the addition of an adenylyl (adenosine 5'-monophosphate; AMP group) to specific residues of target proteins.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0018117	protein adenylylation	The addition of an adenylyl group (adenosine 5'-monophosphate; AMP) to a protein amino acid.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 3se5)

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	NMFIC_NEIMB \| Q7DDR9	:	2g03 3s6a 3sn9 3zlm 5cgl 5ckl 5cmt

2g03	WT FIC
3s6a	WT FIC IN COMPLEX WITH AMPPNP
3sn9	FIC MUTANT SE/AA IN COMPLEX WITH AMPPNP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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