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(-) Description

Title :  CRYSTAL STRUCTURE OF MALIC ENZYME FROM PYROCOCCUS HORIKOSHII OT3
 
Authors :  N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Jan 05  (Deposition) - 21 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Malic Enzyme, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Nppsfa, National Project On Protein Structural And Functional Analyses, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Lokanath, N. Kunishima
Crystal Structure Of Malic Enzyme From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE OXIDOREDUCTASE
    Chains: A, B
    EC Number: 1.1.1.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: 21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: MALIC ENZYME

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 11)

Asymmetric/Biological Unit (1, 11)
No.NameCountTypeFull Name
1MSE11Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WW8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WW8)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Phe A:14 -Pro A:15
2Thr A:39 -Pro A:40
3Ser A:139 -Pro A:140
4Asn A:297 -Pro A:298
5Phe B:14 -Pro B:15
6Thr B:39 -Pro B:40
7Ser B:139 -Pro B:140
8Asn B:297 -Pro B:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WW8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WW8)

(-) Exons   (0, 0)

(no "Exon" information available for 1WW8)

(-) 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:433
 aligned with O59029_PYRHO | O59029 from UniProtKB/TrEMBL  Length:439

    Alignment length:433
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430   
         O59029_PYRHO     1 MIREKALEFHKNNFPGNGKIEVIPKVSLESREELTLAYTPGVAEPCKEIARDPGKVYEYTSKGNLVAVVSDGSRILGLGNIGPLAGLPVMEGKALLFKRFGGVDAFPIMIKEQEPNKFIDIVKAIAPTFGGINLEDIASPKCFYILERLREELDIPVFHDDQQGTAAVVLAGLLNALKVVGKKISEITLALFGAGAAGFATLRILTEAGVKPENVRVVELVNGKPRILTSDLDLEKLFPYRGWLLKKTNGENIEGGPQEALKDADVLISFTRPGPGVIKPQWIEKMNEDAIVFPLANPVPEILPEEAKKAGARIVATGRSDYPNQINNLLGFPGIFRGALDVRARTITDSMIIAAAKAIASIVEEPSEENIIPSPLNPIVYAREARAVAEEAMKEGVARTKVKGEWVEEHTIRLIEFYENVIAPINKKRREYS 433
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -1ww8A01 A:2-159 Aminoacid dehydrogenase-like, N-terminal domain. Chain A                                                                                      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.........eeeee.....hhhhhhhhh...hhhhhhhhhhh..hhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh.hhh.eeeeeee..eeee.....hhhhhh..hhhhhh.........hhhhhhh...eeee.........hhhhhh.....eeeee........hhhhhhhh.eeee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww8 A   1 mIREKALEFHKNNFPGNGKIEVIPKVSLESREELTLAYTPGVAEPCKEIARDPGKVYEYTSKGNLVAVVSDGSRILGLGNIGPLAGLPVmEGKALLFKRFGGVDAFPImIKEQEPNKFIDIVKAIAPTFGGINLEDIASPKCFYILERLREELDIPVFHDDQQGTAAVVLAGLLNALKVVGKKISEITLALFGAGAAGFATLRILTEAGVKPENVRVVELVNGKPRILTSDLDLEKLFPYRGWLLKKTNGENIEGGPQEALKDADVLISFTRPGPGVIKPQWIEKmNEDAIVFPLANPVPEILPEEAKKAGARIVATGRSDYPNQINNLLGFPGIFRGALDVRARTITDSmIIAAAKAIASIVEEPSEENIIPSPLNPIVYAREARAVAEEAmKEGVARTKVKGEWVEEHTIRLIEFYENVIAPINKKRREYS 433
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     | 290       300       310       320       330       340       350|      360       370       380       390  |    400       410       420       430   
                            |                                                                                       90-MSE            109-MSE                                                                                                                                                                          286-MSE                                                          351-MSE                                   393-MSE                                    
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:433
 aligned with O59029_PYRHO | O59029 from UniProtKB/TrEMBL  Length:439

    Alignment length:433
                                    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       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432   
         O59029_PYRHO     3 REKALEFHKNNFPGNGKIEVIPKVSLESREELTLAYTPGVAEPCKEIARDPGKVYEYTSKGNLVAVVSDGSRILGLGNIGPLAGLPVMEGKALLFKRFGGVDAFPIMIKEQEPNKFIDIVKAIAPTFGGINLEDIASPKCFYILERLREELDIPVFHDDQQGTAAVVLAGLLNALKVVGKKISEITLALFGAGAAGFATLRILTEAGVKPENVRVVELVNGKPRILTSDLDLEKLFPYRGWLLKKTNGENIEGGPQEALKDADVLISFTRPGPGVIKPQWIEKMNEDAIVFPLANPVPEILPEEAKKAGARIVATGRSDYPNQINNLLGFPGIFRGALDVRARTITDSMIIAAAKAIASIVEEPSEENIIPSPLNPIVYAREARAVAEEAMKEGVARTKVKGEWVEEHTIRLIEFYENVIAPINKKRREYSKA 435
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ww8B01 B:3-159 Aminoacid dehydrogenase-like, N-terminal domain. Chain A                                                                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------malic-1ww8B03 B:111-150                 -----------Malic_M-1ww8B01 B:162-393                                                                                                                                                                                                               ------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------malic-1ww8B04 B:111-150                 -----------Malic_M-1ww8B02 B:162-393                                                                                                                                                                                                               ------------------------------------------ Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------malic-1ww8B05 B:111-150                 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------malic-1ww8B06 B:111-150                 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhh.........eeeee.....hhhhhhhhh...hhhhhhhhhhh..hhhhhhhhh.eeeeee...........hhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhh..hhhhh.eeee..hhhhhhhhhhhhhh..hhh.eeeeeee..eeee.....hhhhhh..hhhhhh.........hhhhhhh...eeee.........hhhhhh......eeee........hhhhhhhh...ee...........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ww8 B   3 REKALEFHKNNFPGNGKIEVIPKVSLESREELTLAYTPGVAEPCKEIARDPGKVYEYTSKGNLVAVVSDGSRILGLGNIGPLAGLPVmEGKALLFKRFGGVDAFPImIKEQEPNKFIDIVKAIAPTFGGINLEDIASPKCFYILERLREELDIPVFHDDQQGTAAVVLAGLLNALKVVGKKISEITLALFGAGAAGFATLRILTEAGVKPENVRVVELVNGKPRILTSDLDLEKLFPYRGWLLKKTNGENIEGGPQEALKDADVLISFTRPGPGVIKPQWIEKmNEDAIVFPLANPVPEILPEEAKKAGARIVATGRSDYPNQINNLLGFPGIFRGALDVRARTITDSmIIAAAKAIASIVEEPSEENIIPSPLNPIVYAREARAVAEEAmKEGVARTKVKGEWVEEHTIRLIEFYENVIAPINKKRREYSKA 435
                                    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       272       282   |   292       302       312       322       332       342       352       362       372       382       392|      402       412       422       432   
                                                                                                                  90-MSE            109-MSE                                                                                                                                                                          286-MSE                                                          351-MSE                                   393-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  (0, 0)

(no "SCOP Domain" information available for 1WW8)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: malic] (9)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O59029_PYRHO | O59029)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004471    malate dehydrogenase (decarboxylating) (NAD+) activity    Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH + H+.
    GO:0004470    malic enzyme activity    Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0006108    malate metabolic process    The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        O59029_PYRHO | O59029: 2dvm

(-) Related Entries Specified in the PDB File

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