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(-) Description

Title :  AQUIFEX AEOLICUS KDO8PS R106G MUTANT IN COMPLEX WITH 2PGA AND R5P
 
Authors :  X. Xu, F. Kona, J. Wang, J. Lu, T. Stemmler, D. L. Gatti
Date :  28 Apr 05  (Deposition) - 27 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Kdo8Ps, Kdsa, Catalysis, Loops, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Xu, F. Kona, J. Wang, J. Lu, T. Stemmler, D. L. Gatti
The Catalytic And Conformational Cycle Of Aquifex Aeolicus Kdo8P Synthase: Role Of The L7 Loop
Biochemistry V. 44 12434 2005
PubMed-ID: 16156656  |  Reference-DOI: 10.1021/BI051095Q

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    ChainsA, B
    EC Number2.5.1.55
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidP28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneKDSA
    MutationYES
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
    SynonymPHOSPHO-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

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
12PG2Ligand/Ion2-PHOSPHOGLYCERIC ACID
2CD2Ligand/IonCADMIUM ION
3PO41Ligand/IonPHOSPHATE ION
4R5P1Ligand/IonRIBOSE-5-PHOSPHATE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
12PG4Ligand/Ion2-PHOSPHOGLYCERIC ACID
2CD-1Ligand/IonCADMIUM ION
3PO42Ligand/IonPHOSPHATE ION
4R5P2Ligand/IonRIBOSE-5-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:1048 , ARG A:1049 , SER A:1050 , HIS A:1185 , GLN A:1188 , ASP A:1233 , 2PG A:1268 , CD A:1270 , HOH A:3042BINDING SITE FOR RESIDUE R5P A 1269
2AC2SOFTWAREARG B:2049 , SER B:2050 , HOH B:3032BINDING SITE FOR RESIDUE PO4 B 2269
3AC3SOFTWARECYS A:1011 , HIS A:1185 , GLU A:1222 , ASP A:1233 , R5P A:1269BINDING SITE FOR RESIDUE CD A 1270
4AC4SOFTWARECYS B:2011 , HIS B:2185 , GLU B:2222 , ASP B:2233 , 2PG B:2268BINDING SITE FOR RESIDUE CD B 2270
5AC5SOFTWARELYS A:1041 , SER A:1043 , LYS A:1046 , ASP A:1081 , GLN A:1099 , PRO A:1101 , ALA A:1102 , LYS A:1124 , ARG A:1154 , HIS A:1185 , PHE A:1220 , R5P A:1269 , HOH A:3042BINDING SITE FOR RESIDUE 2PG A 1268
6AC6SOFTWARELYS B:2041 , SER B:2043 , LYS B:2046 , ASP B:2081 , GLN B:2099 , PRO B:2101 , ALA B:2102 , LYS B:2124 , ARG B:2154 , HIS B:2185 , PHE B:2220 , GLU B:2222 , CD B:2270 , HOH B:3030 , HOH B:3105BINDING SITE FOR RESIDUE 2PG B 2268

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZJI)

(-) 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:257
 aligned with KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:263
                                    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   
          KDSA_AQUAE      2 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1zjia_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                           SCOP domains
               CATH domains 1zjiA00 A:1002-1264 Aldolase class I                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.hhhhh...------..hhhhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zji A 1002 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCGQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPG------GGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 1264
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261   
                                                                                                                                                                                                                      1191   1198                                                                  

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
          KDSA_AQUAE      3 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1zjib_ B: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                          SCOP domains
               CATH domains 1zjiB00 B:2003-2264 Aldolase class I                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) DAHP_synth_1-1zjiB01 B:2003-2259                                                                                                                                                                                                                                 ----- Pfam domains (1)
           Pfam domains (2) DAHP_synth_1-1zjiB02 B:2003-2259                                                                                                                                                                                                                                 ----- Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.........------.hhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zji B 2003 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCGQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPG------GGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 2264
                                  2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122      2132      2142      2152      2162      2172      2182        |-     |2202      2212      2222      2232      2242      2252      2262  
                                                                                                                                                                                                                     2191   2198                                                                  

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KDSA_AQUAE | O66496)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSA_AQUAE | O664961fwn 1fws 1fwt 1fww 1fx6 1fxp 1fxq 1fy6 1jcx 1jcy 1lrn 1lro 1lrq 1pck 1pcw 1pe1 1t8x 1t96 1t99 1zha 2a21 2a2i 2ef9 2nwr 2nws 2nx1 2nx3 2nxg 2nxh 2nxi 3e0i 3e12

(-) Related Entries Specified in the PDB File

1zha