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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CATALYTIC MECHANISM OF CTP:PHOSPHOCHOLINE CYTIDYLYTRANSFERASE FROM STREPTOCOCCUS PNEUMONIAE (LICC)

Authors :   B. -Y. Kwak, M. Yun, H. -W. Park

Date :   12 Sep 01 (Deposition) - 22 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Licc, 3D Structure, Ctp:Phosphocholine Cytidylyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Y. Kwak, Y. M. Zhang, M. Yun, R. J. Heath, C. O. Rock, S. Jackowski, H. W. Park
Structure And Mechanism Of Ctp:Phosphocholine Cytidylyltransferase (Licc) From Streptococcus Pneumoniae.
J. Biol. Chem. V. 277 4343 2002
PubMed-ID: 11706035 | Reference-DOI: 10.1074/JBC.M109163200
(for further references see the PDB file header)

Molecule 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	LICC
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	LICC PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CDC	4	Ligand/Ion	[2-CYTIDYLATE-O'-PHOSPHONYLOXYL]-ETHYL-TRIMETHYL-AMMONIUM
2	MG	4	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:107 , GLU A:216 , ASP A:218 , CDC A:1991	BINDING SITE FOR RESIDUE MG A 1996
2	AC2	SOFTWARE	ASP B:107 , GLU B:216 , ASP B:218 , CDC B:2991 , HOH B:5164	BINDING SITE FOR RESIDUE MG B 2996
3	AC3	SOFTWARE	ASP C:107 , GLU C:216 , ASP C:218 , CDC C:3991	BINDING SITE FOR RESIDUE MG C 3996
4	AC4	SOFTWARE	ASP D:107 , GLU D:216 , ASP D:218 , CDC D:4991 , HOH D:5165	BINDING SITE FOR RESIDUE MG D 4996
5	AC5	SOFTWARE	LEU A:11 , ALA A:12 , ALA A:13 , GLY A:14 , TYR A:82 , TYR A:85 , ASN A:86 , ASN A:87 , SER A:90 , ALA A:106 , ASP A:107 , TRP A:136 , TYR A:190 , ASP A:192 , GLU A:216 , ASP A:218 , MG A:1996 , HOH A:5004 , HOH A:5177	BINDING SITE FOR RESIDUE CDC A 1991
6	AC6	SOFTWARE	PRO A:21 , LEU B:11 , ALA B:12 , ALA B:13 , GLY B:14 , LYS B:28 , TYR B:82 , TYR B:85 , ASN B:86 , ASN B:87 , SER B:90 , ALA B:106 , ASP B:107 , TRP B:136 , TYR B:190 , ASP B:192 , GLU B:216 , ASP B:218 , MG B:2996 , HOH B:5153	BINDING SITE FOR RESIDUE CDC B 2991
7	AC7	SOFTWARE	LEU C:11 , ALA C:12 , ALA C:13 , GLY C:14 , TYR C:82 , TYR C:85 , ASN C:86 , ASN C:87 , SER C:90 , ALA C:106 , ASP C:107 , TRP C:136 , TYR C:190 , ASP C:192 , GLU C:216 , ASP C:218 , MG C:3996	BINDING SITE FOR RESIDUE CDC C 3991
8	AC8	SOFTWARE	PRO C:21 , GLU C:24 , LEU D:11 , ALA D:12 , ALA D:13 , GLY D:14 , LYS D:28 , TYR D:82 , TYR D:85 , ASN D:86 , ASN D:87 , SER D:90 , ALA D:106 , ASP D:107 , TRP D:136 , TYR D:190 , ASP D:192 , GLU D:216 , ASP D:218 , MG D:4996 , HOH D:5166	BINDING SITE FOR RESIDUE CDC D 4991

(no "SS Bond" information available for 1JYL)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:20	-	Pro A:21
2	Arg B:20	-	Pro B:21
3	Arg C:20	-	Pro C:21
4	Arg D:20	-	Pro D:21

(no "SAP(SNP)/Variant" information available for 1JYL)

(no "PROSITE Motif" information available for 1JYL)

(no "Exon" information available for 1JYL)

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:228
 aligned with A0A0H2UQB5_S | A0A0H2UQB5 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                              1                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         A0A0H2UQB5_S     - --MKAIILAAGLGTRLRPMTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 226
               SCOP domains d1jyla_ A: CTP:phosphocholine cytidylytransferase LicC                                                                                                                                                                               SCOP domains
               CATH domains 1jylA00 A:4-231 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhh......hhhhh.....hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.eeee........hhhhhhhh......eeeee..eee............ee..eeeeeeeeeeeeee.....eeeeeeeeeeeee...eeeehhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..ee.......eee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jyl A   4 IRVKAIILAAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with A0A0H2UQB5_S | A0A0H2UQB5 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                              1                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         A0A0H2UQB5_S     - --MKAIILAAGLGTRLRPMTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 226
               SCOP domains d1jylb_ B: CTP:phosphocholine cytidylytransferase LicC                                                                                                                                                                               SCOP domains
               CATH domains 1jylB00 B:4-231 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhh......hhhhh.....hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.eeee........hhhhhhhh......eeeee..eee............ee..eeeeeeeeeeeeee.....eeeeeeeeeeeee...eeeehhhhhhhhhhhhhhhhhhh.......hhhhhh.......ee.......eee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jyl B   4 IRVKAIILAAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain C from PDB  Type:PROTEIN  Length:228
 aligned with A0A0H2UQB5_S | A0A0H2UQB5 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                              1                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         A0A0H2UQB5_S     - --MKAIILAAGLGTRLRPMTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 226
               SCOP domains d1jylc_ C: CTP:phosphocholine cytidylytransferase LicC                                                                                                                                                                               SCOP domains
               CATH domains 1jylC00 C:4-231 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhh......hhhhh.....hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.eeee........hhhhhhhhhhhh..eeeee..eee............ee..eeeeeeeeeeeeee.....eeeeeeeeeeeee...eeeehhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..ee.......eee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jyl C   4 IRVKAIILAAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain D from PDB  Type:PROTEIN  Length:228
 aligned with A0A0H2UQB5_S | A0A0H2UQB5 from UniProtKB/TrEMBL  Length:229

    Alignment length:228
                              1                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218        
         A0A0H2UQB5_S     - --MKAIILAAGLGTRLRPMTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 226
               SCOP domains d1jyld_ D: CTP:phosphocholine cytidylytransferase LicC                                                                                                                                                                               SCOP domains
               CATH domains 1jylD00 D:4-231 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....hhhhh................hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.eeee........hhhhhhh.......eeeee..eee............ee..eeeeeeeeeeeeee.....eeeeeeeeeeeee...eeeehhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh..ee.......eee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jyl D   4 IRVKAIILAAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKYGVRLVFNDKYADYNNFYSLYLVKEELANSYVIDADNYLFKNMFRNDLTRSTYFSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK 231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Nucleotide-diphospho-sugar transferases (408)

Superfamily: Nucleotide-diphospho-sugar transferases (408)

Family: Cytidylytransferase (43)

Protein domain: CTP:phosphocholine cytidylytransferase LicC (2)

Pneumococcus (Streptococcus pneumoniae) [TaxId: 1313] (2)

1a	d1jyla_	A:
1b	d1jylb_	B:
1c	d1jylc_	C:
1d	d1jyld_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Homologous Superfamily: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Streptococcus pneumoniae. Organism_taxid: 1313. (5)

1a	1jylA00	A:4-231
1b	1jylD00	D:4-231
1c	1jylB00	B:4-231
1d	1jylC00	C:4-231

(no "Pfam Domain" information available for 1JYL)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1JYL)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:20 - Pro A:21	[ RasMol ]
		Arg B:20 - Pro B:21	[ RasMol ]
		Arg C:20 - Pro C:21	[ RasMol ]
		Arg D:20 - Pro D:21	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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