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(-) Description

Title :  AQUIFEX AEOLICUS KDO8PS IN COMPLEX WITH PEP, A5P, ZN2+
 
Authors :  F. Kona, X. Xu, J. Lu, P. Martin, D. L. Gatti
Date :  22 Jun 05  (Deposition) - 04 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Kdo8P, Kdo8Ps, Pep, A5P, Zn2+, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Kona, P. Tao, P. Martin, X. Xu, D. L. Gatti
Electronic Structure Of The Metal Center In The Cd(2+), Zn(2+), And Cu(2+) Substituted Forms Of Kdo8P Synthase: Implications For Catalysis.
Biochemistry V. 48 3610 2009
PubMed-ID: 19228070  |  Reference-DOI: 10.1021/BI801955H

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
    Chains: A, B
    EC Number: 2.5.1.55
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KDSA
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    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

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1A5P2Ligand/IonARABINOSE-5-PHOSPHATE
2PEP2Ligand/IonPHOSPHOENOLPYRUVATE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1A5P4Ligand/IonARABINOSE-5-PHOSPHATE
2PEP4Ligand/IonPHOSPHOENOLPYRUVATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1011 , HIS A:1185 , GLU A:1222 , ASP A:1233 , A5P A:1269BINDING SITE FOR RESIDUE ZN A 1270
2AC2SOFTWARECYS B:2011 , HIS B:2185 , GLU B:2222 , ASP B:2233 , A5P B:2269BINDING SITE FOR RESIDUE ZN B 2270
3AC3SOFTWARELYS A:1041 , SER A:1043 , LYS A:1046 , GLN A:1099 , PRO A:1101 , ALA A:1102 , LYS A:1124 , ARG A:1154 , HIS A:1185 , PHE A:1220 , A5P A:1269 , HOH A:3017 , HOH A:3031 , HOH A:3088BINDING SITE FOR RESIDUE PEP A 1268
4AC4SOFTWARELYS 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 , A5P B:2269 , HOH B:3044 , HOH B:3051 , HOH B:3093BINDING SITE FOR RESIDUE PEP B 2268
5AC5SOFTWAREASN A:1048 , ARG A:1049 , SER A:1050 , ARG A:1154 , HIS A:1185 , GLN A:1188 , SER A:1197 , ASP A:1233 , PEP A:1268 , ZN A:1270 , HOH A:3017 , HOH A:3118 , ARG B:2106BINDING SITE FOR RESIDUE A5P A 1269
6AC6SOFTWAREARG A:1106 , LYS B:2046 , ASN B:2048 , ARG B:2049 , SER B:2050 , HIS B:2185 , SER B:2232 , ASP B:2233 , PEP B:2268 , ZN B:2270 , HOH B:3044 , HOH B:3055 , HOH B:3062 , HOH B:3840BINDING SITE FOR RESIDUE A5P B 2269

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A2I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A2I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A2I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A2I)

(-) Exons   (0, 0)

(no "Exon" information available for 2A2I)

(-) 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:263
 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 d2a2ia_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                           SCOP domains
               CATH domains 2a2iA00 A:1002-1264 Aldolase class I                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.hhh.ee........ee...hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2a2i A 1002 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 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   


Chain B from PDB  Type:PROTEIN  Length:255
 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 d2a2ib_ B: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                          SCOP domains
               CATH domains 2a2iB00 B:2003-2264 Aldolase class I                                                                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.hhhhh...-------.hhhhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2a2i B 2003 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPG-------GMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 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    2199
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A2I)

(-) 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

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UniProtKB/Swiss-Prot
        KDSA_AQUAE | O66496: 1fwn 1fws 1fwt 1fww 1fx6 1fxp 1fxq 1fy6 1jcx 1jcy 1lrn 1lro 1lrq 1pck 1pcw 1pe1 1t8x 1t96 1t99 1zha 1zji 2a21 2ef9 2nwr 2nws 2nx1 2nx3 2nxg 2nxh 2nxi 3e0i 3e12

(-) Related Entries Specified in the PDB File

2a21