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(-) Description

Title :  CRYSTAL STRUCTURE OF KDO-8-PHOSPHATE SYNTHASE
 
Authors :  Structural Genomix
Date :  23 Oct 03  (Deposition) - 11 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
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

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 2.5.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KDSA, HI1557
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: PHOSPHO-2- DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D- MANNO-OCTULOSONIC ACID 8- PHOSPHATE SYNTHETASE, KDO-8-PHOSPHATE SYNTHETASE, KDO 8-P SYNTHASE, KDOPS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 36)

Asymmetric/Biological Unit (1, 36)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1O60)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O60)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O60)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O60)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O60)

(-) Exons   (0, 0)

(no "Exon" information available for 1O60)

(-) 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:269
 aligned with KDSA_HAEIN | P45251 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:281
                                    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       261       271       281 
           KDSA_HAEIN     2 QNKIVKIGNIDVANDKPFVLFGGMNVLESRDMAMQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGMEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAMAKTGAVINVKKPQFLSPSQMGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDMLGFSVMKKASKGSPVIFDVTHSLQCRDPFGAASSGRRAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQMKAIDDLVKSFPELDT 282
               SCOP domains d1o60a_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                                             SCOP domains
               CATH domains 1o60A00 A:2-282 Aldolase class I                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeeehhhhh.------------..hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o60 A   2 QNKIVKIGNIDVANDKPFVLFGGmNVLESRDmAmQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGmEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAmAKTGAVINVKKPQFLSPSQmGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDmLGFSVmKKASKGSPVIFDVTHSLQ------------RAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQmKAIDDLVKSFPELDT 282
                                    11        21   |    31 | |    41        51        61        71  |     81        91       101       111       121      |131       141      |151       161       171       181     | 191       201   |     -      |221       231       241       251       261     | 271       281 
                                                  25-MSE  33-MSE                                   74-MSE                                               128-MSE             148-MSE                          181-MSE |               205          218                                              267-MSE           
                                                            35-MSE                                                                                                                                                 187-MSE                                                                                           


Chain B from PDB  Type:PROTEIN  Length:269
 aligned with KDSA_HAEIN | P45251 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:281
                                    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       261       271       281 
           KDSA_HAEIN     2 QNKIVKIGNIDVANDKPFVLFGGMNVLESRDMAMQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGMEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAMAKTGAVINVKKPQFLSPSQMGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDMLGFSVMKKASKGSPVIFDVTHSLQCRDPFGAASSGRRAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQMKAIDDLVKSFPELDT 282
               SCOP domains d1o60b_ B: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                                             SCOP domains
               CATH domains 1o60B00 B:2-282 Aldolase class I                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeeehhhhh.------------..hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o60 B   2 QNKIVKIGNIDVANDKPFVLFGGmNVLESRDmAmQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGmEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAmAKTGAVINVKKPQFLSPSQmGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDmLGFSVmKKASKGSPVIFDVTHSLQ------------RAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQmKAIDDLVKSFPELDT 282
                                    11        21   |    31 | |    41        51        61        71  |     81        91       101       111       121      |131       141      |151       161       171       181     | 191       201   |     -      |221       231       241       251       261     | 271       281 
                                                  25-MSE  33-MSE                                   74-MSE                                               128-MSE             148-MSE                          181-MSE |               205          218                                              267-MSE           
                                                            35-MSE                                                                                                                                                 187-MSE                                                                                           


Chain C from PDB  Type:PROTEIN  Length:269
 aligned with KDSA_HAEIN | P45251 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:281
                                    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       261       271       281 
           KDSA_HAEIN     2 QNKIVKIGNIDVANDKPFVLFGGMNVLESRDMAMQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGMEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAMAKTGAVINVKKPQFLSPSQMGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDMLGFSVMKKASKGSPVIFDVTHSLQCRDPFGAASSGRRAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQMKAIDDLVKSFPELDT 282
               SCOP domains d1o60c_ C: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                                             SCOP domains
               CATH domains 1o60C00 C:2-282 Aldolase class I                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeee.hhhh.------------..hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o60 C   2 QNKIVKIGNIDVANDKPFVLFGGmNVLESRDmAmQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGmEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAmAKTGAVINVKKPQFLSPSQmGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDmLGFSVmKKASKGSPVIFDVTHSLQ------------RAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQmKAIDDLVKSFPELDT 282
                                    11        21   |    31 | |    41        51        61        71  |     81        91       101       111       121      |131       141      |151       161       171       181     | 191       201   |     -      |221       231       241       251       261     | 271       281 
                                                  25-MSE  33-MSE                                   74-MSE                                               128-MSE             148-MSE                          181-MSE |               205          218                                              267-MSE           
                                                            35-MSE                                                                                                                                                 187-MSE                                                                                           


Chain D from PDB  Type:PROTEIN  Length:269
 aligned with KDSA_HAEIN | P45251 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:281
                                    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       261       271       281 
           KDSA_HAEIN     2 QNKIVKIGNIDVANDKPFVLFGGMNVLESRDMAMQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGMEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAMAKTGAVINVKKPQFLSPSQMGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDMLGFSVMKKASKGSPVIFDVTHSLQCRDPFGAASSGRRAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQMKAIDDLVKSFPELDT 282
               SCOP domains d1o60d_ D: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                                             SCOP domains
               CATH domains 1o60D00 D:2-282 Aldolase class I                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) DAHP_synth_1-1o60D01 D:2-276                                                                                                                                                                                                                                                       ------ Pfam domains (1)
           Pfam domains (2) DAHP_synth_1-1o60D02 D:2-276                                                                                                                                                                                                                                                       ------ Pfam domains (2)
           Pfam domains (3) DAHP_synth_1-1o60D03 D:2-276                                                                                                                                                                                                                                                       ------ Pfam domains (3)
           Pfam domains (4) DAHP_synth_1-1o60D04 D:2-276                                                                                                                                                                                                                                                       ------ Pfam domains (4)
         Sec.struct. author ....eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh.....eeeee..ee.....ee...hhhhhhhhhh....eeeehhhhh.------------..hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o60 D   2 QNKIVKIGNIDVANDKPFVLFGGmNVLESRDmAmQVCEAYVKVTEKLGVPYVFKASFDKANRSSIHSYRGPGmEEGLKIFQELKDTFGVKIITDVHEIYQCQPVADVVDIIQLPAFLARQTDLVEAmAKTGAVINVKKPQFLSPSQmGNIVEKIEECGNDKIILCDRGTNFGYDNLIVDmLGFSVmKKASKGSPVIFDVTHSLQ------------RAQVTELARSGLAVGIAGLFLEAHPNPNQAKCDGPSALPLSALEGFVSQmKAIDDLVKSFPELDT 282
                                    11        21   |    31 | |    41        51        61        71  |     81        91       101       111       121      |131       141      |151       161       171       181     | 191       201   |     -      |221       231       241       251       261     | 271       281 
                                                  25-MSE  33-MSE                                   74-MSE                                               128-MSE             148-MSE                          181-MSE |               205          218                                              267-MSE           
                                                            35-MSE                                                                                                                                                 187-MSE
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (KDSA_HAEIN | P45251)
molecular function
    GO:0008676    3-deoxy-8-phosphooctulonate synthase activity    Catalysis of the reaction: D-arabinose 5-phosphate + H(2)O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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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