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(-) Description

Title :  CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA MALIC ENZYME
 
Authors :  D. Dutta, A. Chakrabarty, S. K. Ghosh, A. K. Das
Date :  08 Jul 10  (Deposition) - 20 Jul 11  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chakrabarty, D. Dutta, A. K. Das, S. K. Ghosh
Structural And Functional Characterization Of Entamoeba Histolytica Malic Enzyme
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MALIC ENZYME
    Chains: A, B
    EC Number: 1.1.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EHI_044970, EHME
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 5759

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 28)

Asymmetric/Biological Unit (4, 28)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL8Ligand/IonGLYCEROL
3NA2Ligand/IonSODIUM ION
4SO415Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:183 , LYS A:377 , THR A:379 , ASP A:380 , HOH A:635BINDING SITE FOR RESIDUE SO4 A 488
02AC2SOFTWAREGLN A:30 , LYS A:33 , THR A:434 , HOH A:689 , ARG B:71 , HOH B:503BINDING SITE FOR RESIDUE SO4 A 489
03AC3SOFTWAREARG A:453 , GLN A:457 , HOH A:746BINDING SITE FOR RESIDUE SO4 A 490
04AC4SOFTWARESER A:20 , GLN A:21 , HOH A:671BINDING SITE FOR RESIDUE SO4 A 491
05AC5SOFTWAREGLY A:226 , ALA A:227 , ASP A:252 , SER A:253 , HOH A:741BINDING SITE FOR RESIDUE SO4 A 492
06AC6SOFTWARELYS A:5 , ALA A:6 , HOH A:688BINDING SITE FOR RESIDUE SO4 A 493
07AC7SOFTWAREARG A:376 , ARG A:432BINDING SITE FOR RESIDUE SO4 A 494
08AC8SOFTWARETHR A:348 , ARG A:350 , PHE A:353 , PRO A:354 , ASN A:355 , GLN A:356BINDING SITE FOR RESIDUE NA A 495
09AC9SOFTWARESER A:287 , ILE A:288 , ALA A:289 , LYS A:310 , GLU A:312 , TRP A:313 , LYS A:396 , HOH A:818 , HOH A:819BINDING SITE FOR RESIDUE GOL A 496
10BC1SOFTWAREARG A:101 , ILE A:170 , GLN A:172 , GLY A:228 , SER A:229 , THR A:303 , HOH A:564BINDING SITE FOR RESIDUE GOL A 498
11BC2SOFTWAREPRO A:148 , LYS A:177 , ARG A:269 , ALA B:289BINDING SITE FOR RESIDUE GOL A 499
12BC3SOFTWARELEU A:103 , VAL A:116 , LYS A:120 , ASP A:169 , ASN A:358 , ASN A:359 , HOH A:518 , TYR B:65 , THR B:66BINDING SITE FOR RESIDUE GOL A 497
13BC4SOFTWAREARG A:157 , ASN B:141 , LYS B:142 , GLU B:143BINDING SITE FOR RESIDUE GOL B 500
14BC5SOFTWAREASP A:81 , ARG A:89 , ASP A:187 , ARG A:374BINDING SITE FOR RESIDUE ACT A 502
15BC6SOFTWAREARG B:183 , THR B:379 , ASP B:380BINDING SITE FOR RESIDUE SO4 B 488
16BC7SOFTWAREALA B:227 , ASP B:252 , SER B:253 , GOL B:498 , HOH B:681BINDING SITE FOR RESIDUE SO4 B 489
17BC8SOFTWARESER B:20 , GLN B:21 , HOH B:682BINDING SITE FOR RESIDUE SO4 B 490
18BC9SOFTWAREGLN B:30 , LYS B:33 , HOH B:650BINDING SITE FOR RESIDUE SO4 B 491
19CC1SOFTWAREPRO B:411 , ARG B:453 , HOH B:717BINDING SITE FOR RESIDUE SO4 B 492
20CC2SOFTWARELYS B:5 , PHE B:393 , ASP B:409 , GLU B:410 , PRO B:411 , GLY B:412 , HOH B:611 , HOH B:720BINDING SITE FOR RESIDUE SO4 B 493
21CC3SOFTWAREASN B:75 , ASN B:79 , PHE B:85 , TYR B:86BINDING SITE FOR RESIDUE SO4 B 494
22CC4SOFTWAREASN A:141 , LYS A:142 , GLU A:143 , HOH A:754 , LYS B:315BINDING SITE FOR RESIDUE SO4 B 495
23CC5SOFTWARETHR B:348 , ARG B:350 , PHE B:353 , PRO B:354 , ASN B:355 , GLN B:356BINDING SITE FOR RESIDUE NA B 496
24CC6SOFTWAREGLN B:172 , TYR B:176 , ALA B:227 , ARG B:269 , PHE B:270 , TYR B:271 , ARG B:272 , LYS B:273BINDING SITE FOR RESIDUE GOL B 497
25CC7SOFTWAREARG B:101 , GLN B:172 , GLY B:228 , SER B:229 , SO4 B:489 , HOH B:808 , HOH B:809BINDING SITE FOR RESIDUE GOL B 498
26CC8SOFTWAREASP B:81 , ASP B:187BINDING SITE FOR RESIDUE ACT B 499
27CC9SOFTWAREASN B:91 , LYS B:368 , ASP B:448BINDING SITE FOR RESIDUE ACT B 501
28DC1SOFTWARETYR A:65 , THR A:66 , LEU B:103 , VAL B:116 , LYS B:120 , ASP B:169 , ASN B:358 , HOH B:773BINDING SITE FOR RESIDUE GOL B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NV9)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Thr A:66 -Pro A:67
2Gln A:172 -Pro A:173
3Thr A:303 -Pro A:304
4Pro A:304 -Gly A:305
5Asn A:328 -Pro A:329
6Thr B:66 -Pro B:67
7Gln B:172 -Pro B:173
8Gly B:305 -Pro B:306
9Asn B:328 -Pro B:329

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NV9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NV9)

(-) Exons   (0, 0)

(no "Exon" information available for 3NV9)

(-) 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:486
 aligned with Q9NH04_ENTHI | Q9NH04 from UniProtKB/TrEMBL  Length:487

    Alignment length:486
                                    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       440       450       460       470       480      
         Q9NH04_ENTHI     1 MAQLKADLSNLEECLPSTLSQEQRAVAKTQFYKELAEKVHKFYKGKIQIMPKCTLAGFNWFNAYYTPGVSRISTNIRDNNDSSLFYSLRGNFVGVVSDSTRVLGDGDVTPPGGLGVMEGKALLMKYLGGIDAVPICIDSKNKEGKNDPDAVIEFVQRIQHTFGAINLEDISQPNCYKILDVLRESCDIPVWHDDQQGTASVTLAGLLNALKLVKKDIHECRMVFIGAGSSNTTCLRLIVTAGADPKKIVMFDSKGSLHNGREDIKKDTRFYRKWEICETTNPSKFGSIAEACVGADVLISLSTPGPGVVKAEWIKSMGEKPIVFCCANPVPEIYPYEAKEAGAYIVATGRGDFPNQVNNSVGFPGILKGALIVRARKITDNMAIAASRALAEFAEKRGINPDNIIGTMDEPGIFPKEAADVAMQAIKDGVARVTDLTWQQVYDIAEHDIKEARESAQLLQDSKHIVDFPQETLNECLAYAINKVTG 486
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh.eeeeee....hhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhhhhh..hhh.eeeee..ee....hhhhhhh..hhhhhhhhhhh......hhhhhhh...eeee.........hhhhhhh.....eeee........hhhhhhhh...eeee.........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nv9 A   1 MAQLKADLSNLEECLPSTLSQEQRAVAKTQFYKELAEKVHKFYKGKIQIMPKCTLAGFNWFNAYYTPGVSRISTNIRDNNDSSLFYSLRGNFVGVVSDSTRVLGDGDVTPPGGLGVMEGKALLMKYLGGIDAVPICIDSKNKEGKNDPDAVIEFVQRIQHTFGAINLEDISQPNCYKILDVLRESCDIPVWHDDQQGTASVTLAGLLNALKLVKKDIHECRMVFIGAGSSNTTCLRLIVTAGADPKKIVMFDSKGSLHNGREDIKKDTRFYRKWEICETTNPSKFGSIAEACVGADVLISLSTPGPGVVKAEWIKSMGEKPIVFCCANPVPEIYPYEAKEAGAYIVATGRGDFPNQVNNSVGFPGILKGALIVRARKITDNMAIAASRALAEFAEKRGINPDNIIGTMDEPGIFPKEAADVAMQAIKDGVARVTDLTWQQVYDIAEHDIKEARESAQLLQDSKHIVDFPQETLNECLAYAINKVTG 486
                                    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       440       450       460       470       480      


Chain B from PDB  Type:PROTEIN  Length:486
 aligned with Q9NH04_ENTHI | Q9NH04 from UniProtKB/TrEMBL  Length:487

    Alignment length:486
                                    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       440       450       460       470       480      
         Q9NH04_ENTHI     1 MAQLKADLSNLEECLPSTLSQEQRAVAKTQFYKELAEKVHKFYKGKIQIMPKCTLAGFNWFNAYYTPGVSRISTNIRDNNDSSLFYSLRGNFVGVVSDSTRVLGDGDVTPPGGLGVMEGKALLMKYLGGIDAVPICIDSKNKEGKNDPDAVIEFVQRIQHTFGAINLEDISQPNCYKILDVLRESCDIPVWHDDQQGTASVTLAGLLNALKLVKKDIHECRMVFIGAGSSNTTCLRLIVTAGADPKKIVMFDSKGSLHNGREDIKKDTRFYRKWEICETTNPSKFGSIAEACVGADVLISLSTPGPGVVKAEWIKSMGEKPIVFCCANPVPEIYPYEAKEAGAYIVATGRGDFPNQVNNSVGFPGILKGALIVRARKITDNMAIAASRALAEFAEKRGINPDNIIGTMDEPGIFPKEAADVAMQAIKDGVARVTDLTWQQVYDIAEHDIKEARESAQLLQDSKHIVDFPQETLNECLAYAINKVTG 486
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........hhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh.eeeeee....hhhhh..hhhhhhhhhhhhhhhhhhhhh.eeeeee..........hhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhh..hhhhh.eeee..hhhhhhhhhhhhhh..hhh.eeeee..ee....hhhhhhhhhhhhhhhhhhhh......hhhhhhh...eeee.........hhhhhhh.....eeee........hhhhhhhh...eee..........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nv9 B   1 MAQLKADLSNLEECLPSTLSQEQRAVAKTQFYKELAEKVHKFYKGKIQIMPKCTLAGFNWFNAYYTPGVSRISTNIRDNNDSSLFYSLRGNFVGVVSDSTRVLGDGDVTPPGGLGVMEGKALLMKYLGGIDAVPICIDSKNKEGKNDPDAVIEFVQRIQHTFGAINLEDISQPNCYKILDVLRESCDIPVWHDDQQGTASVTLAGLLNALKLVKKDIHECRMVFIGAGSSNTTCLRLIVTAGADPKKIVMFDSKGSLHNGREDIKKDTRFYRKWEICETTNPSKFGSIAEACVGADVLISLSTPGPGVVKAEWIKSMGEKPIVFCCANPVPEIYPYEAKEAGAYIVATGRGDFPNQVNNSVGFPGILKGALIVRARKITDNMAIAASRALAEFAEKRGINPDNIIGTMDEPGIFPKEAADVAMQAIKDGVARVTDLTWQQVYDIAEHDIKEARESAQLLQDSKHIVDFPQETLNECLAYAINKVTG 486
                                    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       440       450       460       470       480
   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 3NV9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NV9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NV9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9NH04_ENTHI | Q9NH04)
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.
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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  3nv9
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  Q9NH04_ENTHI | Q9NH04
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 Related Entries

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