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(-) Description

Title :  HALOFERAX VOLCANII MALATE SYNTHASE MAGNESIUM/GLYOXYLATE COMPLEX
 
Authors :  B. R. Howard, C. Bracken, A. Neighbor, G. Thomas, K. K. Lamlenn, H. L. Sch F. G. Whitby
Date :  24 Sep 10  (Deposition) - 01 Jun 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  A  (6x)
Keywords :  Tim Barrel, Glyoxylate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Bracken, A. M. Neighbor, K. K. Lamlenn, G. C. Thomas, H. L. Schubert, F. G. Whitby, B. R. Howard
Crystal Structures Of A Halophilic Archaeal Malate Synthase From Haloferax Volcanii And Comparisons With Isoforms A And G.
Bmc Struct. Biol. V. 11 23 2011
PubMed-ID: 21569248  |  Reference-DOI: 10.1186/1472-6807-11-23

(-) Compounds

Molecule 1 - MALATE SYNTHASE
    Chains: A
    EC Number: 2.3.3.9
    Organism Scientific: HALOFERAX VOLCANII
    Organism Taxid: 309800
    Strain: ATCC 29605, DS2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A
Biological Unit 2 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2GLV2Ligand/IonGLYOXYLIC ACID
3K3Ligand/IonPOTASSIUM ION
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GLV6Ligand/IonGLYOXYLIC ACID
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GLV12Ligand/IonGLYOXYLIC ACID
3K-1Ligand/IonPOTASSIUM ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:84 , GLU A:158 , GLY A:189 , GLU A:190 , VAL A:191 , ASP A:192 , PRO A:231 , TRP A:257 , HOH A:439 , HOH A:440 , GLV A:502 , MG A:601BINDING SITE FOR RESIDUE GLV A 501
02AC2SOFTWAREARG A:84 , ASP A:388 , HOH A:440 , GLV A:501BINDING SITE FOR RESIDUE GLV A 502
03AC3SOFTWAREGLU A:158 , ASP A:192 , HOH A:439 , HOH A:440 , GLV A:501BINDING SITE FOR RESIDUE MG A 601
04AC4SOFTWAREARG A:198 , ALA A:227 , K A:801BINDING SITE FOR RESIDUE CL A 701
05AC5SOFTWAREARG A:89 , ASP A:90 , PRO A:92 , ARG A:95BINDING SITE FOR RESIDUE CL A 702
06AC6SOFTWAREARG A:218BINDING SITE FOR RESIDUE CL A 703
07AC7SOFTWAREPRO A:207 , ALA A:208 , HOH A:557BINDING SITE FOR RESIDUE CL A 704
08AC8SOFTWAREGLY A:126 , ILE A:127 , ARG A:170 , HOH A:462 , HOH A:531BINDING SITE FOR RESIDUE CL A 705
09AC9SOFTWAREMET A:197 , SER A:217 , SER A:221 , GLY A:252 , CL A:701BINDING SITE FOR RESIDUE K A 801
10BC1SOFTWAREMET A:173 , LYS A:175 , ASN A:178 , GLU A:181 , HOH A:499BINDING SITE FOR RESIDUE K A 802
11BC2SOFTWAREPRO A:176 , ASN A:178 , ASN A:179 , HOH A:476BINDING SITE FOR RESIDUE K A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OYX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:277 -Ser A:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OYX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OYX)

(-) Exons   (0, 0)

(no "Exon" information available for 3OYX)

(-) 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:348
 aligned with ACEB_HALVD | D4GTL2 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:428
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        
           ACEB_HALVD     5 RHDREFVRTFFTSPTAVEGEDDSAKMLRRAAGLRGMQAPDVWVPDNEDATAPSMRDEGAENIVEVISEQGAEFPGEIHPRMVWHRDSPETRYQGFQHMLDITDPERGAVEHIHGFVIPEVGGIDDWKKADEFFTIVEHEHGLDEGSLAMSVIIESGEAELAMGDLRDEMGKPTNNLERLFLLVDGEVDYTKDMRAMTPTGELPAWPELRHNTSRGASAAGCVAVDGPYDDIRDVEGYRERMTDNQAKGMLGIWSLTPGQVVEANTSPLPPKTGSWLLDADGEEVELASEDGVEAYDGDRLSLEATDGGYELRVGGDARELTADELREELLGLTSYVPSMDDIVDSMEEFEAAKEAGRGAIAMTQSATLRIGGTEIDIEKDRMWDEATYQAAMTPISLFQDVYENRPDQHEELEERYGAGVVERAMEVG 432
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.........hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhh.hhhhhhhh...hhh.eeeeeehhhhhhhhh...........hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh....eeee.hhhhhhhhhhh.............-----------------------------------------------hhhhhh.....hhhhhhhhhhh.---------------------------------.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oyx A   5 RHDREFVRTFFTSPTAVEGEDDSAKMLRRAAGLRGMQAPDVWVPDNEDATAPSMRDEGAENIVEVISEQGAEFPGEIHPRMVWHRDSPETRYQGFQHMLDITDPERGAVEHIHGFVIPEVGGIDDWKKADEFFTIVEHEHGLDEGSLAMSVIIESGEAELAMGDLRDEMGKPTNNLERLFLLVDGEVDYTKDMRAMTPTGELPAWPELRHNTSRGASAAGCVAVDGPYDDIRDVEGYRERMTDNQAKGMLGIWSLTPGQVVEANTSPLPPKTGSWLLDA-----------------------------------------------EELLGLTSYVPSMDDIVDSMEEF---------------------------------WDEATYQAAMTPISLFQDVYENRPDQHEELEERYGAGVVERAMEVG 432
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274        |-         -         -         -         -      |334       344        |-         -         -         -  |    394       404       414       424        
                                                                                                                                                                                                                                                                                                                283                                             331                   353                               387
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3OYX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OYX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3OYX)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (ACEB_HALVD | D4GTL2)
molecular function
    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:0004474    malate synthase activity    Catalysis of the reaction: acetyl-CoA + glyoxylate + H(2)O = (S)-malate + CoA + H(+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006097    glyoxylate cycle    A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
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
        ACEB_HALVD | D4GTL2: 3oyz 3pug 5tao

(-) Related Entries Specified in the PDB File

3oyz 3pug