1VIC - JenaLib

Title :   CRYSTAL STRUCTURE OF CMP-KDO SYNTHETASE

Authors :   Structural Genomix

Date :   01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622 | Reference-DOI: 10.1002/PROT.20541

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:255
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:255
                                                                                                                                                                                                                                                                                      254  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  |  
           KDSB_HAEIN     2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN--   -
               SCOP domains d1vica_ A: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                                                            SCOP domains
               CATH domains 1vicA00 A:2-256 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhh..eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhh...hhhhh......eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vic A   2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAANGS 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   
           KDSB_HAEIN     2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN 254
               SCOP domains d1vicb_ B: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                                                          SCOP domains
               CATH domains 1vicB00 B:2-254 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                  CATH domains
           Pfam domains (1) --CTP_transf_3-1vicB01 B:4-225                                                                                                                                                                                                  ----------------------------- Pfam domains (1)
           Pfam domains (2) --CTP_transf_3-1vicB02 B:4-225                                                                                                                                                                                                  ----------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee.............-----........eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh....eeee..........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vic B   2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMN-----KVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN 254
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       | -   |   181       191       201       211       221       231       241       251   
                                                                                                                                                                                                 169   175

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (KDSB_HAEIN | P44490)

molecular function
	GO:0008690	3-deoxy-manno-octulosonate cytidylyltransferase activity	Catalysis of the reaction: CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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:0033468	CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of CMP-keto-3-deoxy-D-manno-octulosonic acid, a substance composed of the acidic sugar 3-deoxy-D-manno-octulosonic acid in glycosidic linkage with cytidine monophosphate.
	GO:0019294	keto-3-deoxy-D-manno-octulosonic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
	GO:0009103	lipopolysaccharide biosynthetic process	The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	1vic
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	KDSB_HAEIN \| P44490
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	2.7.7.38
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