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(-) Description

Title :  THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES, HERE COMPLEX WITH CMP-NEUAC, CMP-NEUAC COMPLEX
 
Authors :  S. Jelakovic, G. E. Schulz
Date :  10 Jul 01  (Deposition) - 13 Sep 01  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nucleotidyltransferase, Cmp-Kdo Synthetase, Nucleoside Monophosphate Glycosides, Lipopolysaccharide Biosynthesis, Sugar-Activating Enzymes, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Jelakovic, G. E. Schulz
The Structure Of Cmp:2-Keto-3-Deoxy-Manno-Octonic Acid Synthetase And Of Its Complexes With Substrates And Substrate Analogs
J. Mol. Biol. V. 312 143 2001
PubMed-ID: 11545592  |  Reference-DOI: 10.1006/JMBI.2001.4948
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KPSU
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: K5
    Synonym: CMP-KDO SYNTHETASE, CKS, CMP-2-KETO-3- DEOXYOCTULOSONIC ACID SYNTHETASE, CMP-2-KETO-3-DEOXY-MANNO -OCTONIC ACID SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:19 , GLN B:96 , ASP B:98 , GLU B:99 , GLY B:174 , GLY B:223 , VAL B:224 , ASP B:225 , C5P B:1242BINDING SITE FOR RESIDUE SIA B1243
2AC2SOFTWAREPRO B:8 , ALA B:9 , ARG B:10 , LYS B:19 , HIS B:73 , GLU B:74 , SER B:75 , ARG B:79 , GLN B:96 , GLY B:97 , ASP B:98 , SIA B:1243BINDING SITE FOR RESIDUE C5P B1242

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1H7T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:158 -Pro A:159
2Ile B:158 -Pro B:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H7T)

(-) Exons   (0, 0)

(no "Exon" information available for 1H7T)

(-) Sequences/Alignments

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:245
 aligned with KPSU5_ECOLX | P42216 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
          KPSU5_ECOLX     2 SKAVIVIPARYGSSRLPGKPLLDIVGKPMIQHVYERALQVAGVAEVWVATDDPRVEQAVQAFGGKAIMTRNDHESGTDRLVEVMHKVEADIYINLQGDEPMIRPRDVETLLQGMRDDPALPVATLCHAISAAEAAEPSTVKVVVNTRQDALYFSRSPIPYPRNAEKARYLKHVGIYAYRRDVLQNYSQLPESMPEQAESLEQLRLMNAGINIRTFEVAATGPGVDTPACLEKVRALMAQELAENA 246
               SCOP domains d1h7ta_ A: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                                                  SCOP domains
               CATH domains 1h7tA00 A:1-245 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..............ee..eehhhhhhhhhh......eeeeee.hhhhhhhhhh...eeee......hhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh....eeeeeeeehhhhhh.....eeee.....eeeee........hhhhh.eeeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h7t A   1 SKAVIVIPARYGSSRLPGKPLLDIVGKPMIQHVYERALQVAGVAEVWVATDDPRVEQAVQAFGGKAIMTRNDHESGTDRLVEVMHKVEADIYINLQGDEPMIRPRDVETLLQGMRDDPALPVATLCHAISAAEAAEPSTVKVVVNTRQDALYFSRSPIPYPRNAEKARYLKHVGIYAYRRDVLQNYSQLPESMPEQAESLEQLRLMNAGINIRTFEVAATGPGVDTPACLEKVRALMAQELAENA 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with KPSU5_ECOLX | P42216 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:241
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241 
          KPSU5_ECOLX     2 SKAVIVIPARYGSSRLPGKPLLDIVGKPMIQHVYERALQVAGVAEVWVATDDPRVEQAVQAFGGKAIMTRNDHESGTDRLVEVMHKVEADIYINLQGDEPMIRPRDVETLLQGMRDDPALPVATLCHAISAAEAAEPSTVKVVVNTRQDALYFSRSPIPYPRNAEKARYLKHVGIYAYRRDVLQNYSQLPESMPEQAESLEQLRLMNAGINIRTFEVAATGPGVDTPACLEKVRALMAQEL 242
               SCOP domains d1h7tb_ B: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                                              SCOP domains
               CATH domains 1h7tB00 B:1-241 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........hhhh.ee..eehhhhhhhhhh......eeeeee.hhhhhhhhhhh...eee......hhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh....eeeeeeeehhhhhh.....eeee.....eeeee........hhhhh.eeeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee.........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h7t B   1 SKAVIVIPARYGSSRLPGKPLLDIVGKPMIQHVYERALQVAGVAEVWVATDDPRVEQAVQAFGGKAIMTRNDHESGTDRLVEVMHKVEADIYINLQGDEPMIRPRDVETLLQGMRDDPALPVATLCHAISAAEAAEPSTVKVVVNTRQDALYFSRSPIPYPRNAEKARYLKHVGIYAYRRDVLQNYSQLPESMPEQAESLEQLRLMNAGINIRTFEVAATGPGVDTPACLEKVRALMAQEL 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1H7T)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KPSU5_ECOLX | P42216)
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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KPSU5_ECOLX | P42216: 1gq9 1gqc 1h6j 1h7e 1h7f 1h7g 1h7h

(-) Related Entries Specified in the PDB File

1h6j THE THREE-DIMENSIONAL STRUCTURE OF CAPSULE- SPECIFIC CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE FROM ESCHERICHIA COLI
1h7e THE STRUCTURE OF CMP:2-KETO-3-DEOXY- MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES
1h7f THE STRUCTURE OF CMP:2-KETO-3-DEOXY- MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES
1h7g THE STRUCTURE OF CMP:2-KETO-3-DEOXY- MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES
1h7h THE STRUCTURE OF CMP:2-KETO-3-DEOXY- MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES