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(-) Description

Title :  CRYSTAL STRUCTURE OF MALIC ENZYME FROM ASCARIS SUUM COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE
 
Authors :  D. E. Coleman, G. S. Jagannatha, E. J. Goldsmith, P. F. Cook, B. G. Harris
Date :  29 Apr 02  (Deposition) - 08 May 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Coleman, G. S. Rao, E. J. Goldsmith, P. F. Cook, B. G. Harris
Crystal Structure Of The Malic Enzyme From Ascaris Suum Complexed With Nicotinamide Adenine Dinucleotide At 2. 3 A Resolution.
Biochemistry V. 41 6928 2002
PubMed-ID: 12033925  |  Reference-DOI: 10.1021/BI0255120

(-) Compounds

Molecule 1 - NAD-DEPENDENT MALIC ENZYME
    Chains: A, B
    EC Number: 1.1.1.38
    Organism Common: PIG ROUNDWORM
    Organism Scientific: ASCARIS SUUM
    Organism Taxid: 6253
    Synonym: NAD-ME

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:275 , THR A:299 , PHE A:326 , GLY A:327 , ALA A:328 , GLY A:329 , ALA A:330 , ALA A:331 , ASP A:361 , ILE A:362 , ALA A:405 , SER A:406 , VAL A:408 , LEU A:432 , SER A:433 , ASN A:434 , GLY A:459 , GLY A:477 , ASN A:479 , HOH A:2013BINDING SITE FOR RESIDUE NAD A 1001
2AC2SOFTWAREASN B:275 , THR B:299 , PHE B:326 , ALA B:328 , GLY B:329 , ALA B:330 , ALA B:331 , ASP B:361 , ILE B:362 , ALA B:405 , SER B:406 , VAL B:408 , LEU B:432 , SER B:433 , ASN B:434 , GLY B:459 , GLY B:477 , ASN B:479BINDING SITE FOR RESIDUE NAD B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:434 -Pro A:435
2Tyr A:555 -Pro A:556
3Asn B:434 -Pro B:435
4Tyr B:555 -Pro B:556

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MALIC_ENZYMESPS00331 Malic enzymes signature.MAOM_ASCSU330-346
 		  2A:292-308
B:292-308
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MALIC_ENZYMESPS00331 Malic enzymes signature.MAOM_ASCSU330-346
 		  4A:292-308
B:292-308

(-) Exons   (0, 0)

(no "Exon" information available for 1LLQ)

(-) 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:599
 aligned with MAOM_ASCSU | P27443 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:599
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629         
           MAOM_ASCSU    40 SVAHHEDVYSHNLPPMDEKEMALYKLYRPERVTPKKRSAELLKEPRLNKGMGFSLYERQYLGLHGLLPPAFMTQEQQAYRVITKLREQPNDLARYIQLDGLQDRNEKLFYRVVCDHVKELMPIVYTPTVGLACQNFGYIYRKPKGLYITINDNSVSKIYQILSNWHEEDVRAIVVTDGERILGLGDLGAYGIGIPVGKLALYVALGGVQPKWCLPVLLDVGTNNMDLLNDPFYIGLRHKRVRGKDYDTLLDNFMKACTKKYGQKTLIQFEDFANPNAFRLLDKYQDKYTMFNDDIQGTASVIVAGLLTCTRVTKKLVSQEKYLFFGAGAASTGIAEMIVHQMQNEGISKEEACNRIYLMDIDGLVTKNRKEMNPRHVQFAKDMPETTSILEVIRAARPGALIGASTVRGAFNEEVIRAMAEINERPIIFALSNPTSKAECTAEEAYTFTNGAALYASGSPFPNFELNGHTYKPGQGNNAYIFPGVALGTILFQIRHVDNDLFLLAAKKVASCVTEDSLKVGRVYPQLKEIREISIQIAVEMAKYCYKNGTANLYPQPEDLEKYVRAQVYNTEYEELINATYDWPEQDMRHGFPVPVVRH 638
               SCOP domains d1llqa2 A:2-295 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                           d1llqa1 A:296-600 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1llqA04 A:294-478 NAD(P)-binding Rossmann-like Domain                                                                                                                                    -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh........hhhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh........eeee.hhhhhhhhhhhhhh.......eeeee..........hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee....hhhhhhh............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeee..hhhhhhhhhhhhhhhhh.......hhh.eeeee..ee........hhhhhh.........hhhhhhhhhh..eeee........hhhhhhhhhhhh...eeee...hhhhh..hhhhhhhh.....eeee......eee..eee..ee.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh.................hhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MALIC_ENZYMES    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1llq A   2 SVAHHEDVYSHNLPPMDEKEMALYKLYRPERVTPKKRSAELLKEPRLNKGMGFSLYERQYLGLHGLLPPAFMTQEQQAYRVITKLREQPNDLARYIQLDGLQDRNEKLFYRVVCDHVKELMPIVYTPTVGLACQNFGYIYRKPKGLYITINDNSVSKIYQILSNWHEEDVRAIVVTDGERILGLGDLGAYGIGIPVGKLALYVALGGVQPKWCLPVLLDVGTNNMDLLNDPFYIGLRHKRVRGKDYDTLLDNFMKACTKKYGQKTLIQFEDFANPNAFRLLDKYQDKYTMFNDDIQGTASVIVAGLLTCTRVTKKLVSQEKYLFFGAGAASTGIAEMIVHQMQNEGISKEEACNRIYLMDIDGLVTKNRKEMNPRHVQFAKDMPETTSILEVIRAARPGALIGASTVRGAFNEEVIRAMAEINERPIIFALSNPTSKAECTAEEAYTFTNGAALYASGSPFPNFELNGHTYKPGQGNNAYIFPGVALGTILFQIRHVDNDLFLLAAKKVASCVTEDSLKVGRVYPQLKEIREISIQIAVEMAKYCYKNGTANLYPQPEDLEKYVRAQVYNTEYEELINATYDWPEQDMRHGFPVPVVRH 600
                                    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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591         


Chain B from PDB  Type:PROTEIN  Length:592
 aligned with MAOM_ASCSU | P27443 from UniProtKB/Swiss-Prot  Length:643

    Alignment length:592
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629  
           MAOM_ASCSU    40 SVAHHEDVYSHNLPPMDEKEMALYKLYRPERVTPKKRSAELLKEPRLNKGMGFSLYERQYLGLHGLLPPAFMTQEQQAYRVITKLREQPNDLARYIQLDGLQDRNEKLFYRVVCDHVKELMPIVYTPTVGLACQNFGYIYRKPKGLYITINDNSVSKIYQILSNWHEEDVRAIVVTDGERILGLGDLGAYGIGIPVGKLALYVALGGVQPKWCLPVLLDVGTNNMDLLNDPFYIGLRHKRVRGKDYDTLLDNFMKACTKKYGQKTLIQFEDFANPNAFRLLDKYQDKYTMFNDDIQGTASVIVAGLLTCTRVTKKLVSQEKYLFFGAGAASTGIAEMIVHQMQNEGISKEEACNRIYLMDIDGLVTKNRKEMNPRHVQFAKDMPETTSILEVIRAARPGALIGASTVRGAFNEEVIRAMAEINERPIIFALSNPTSKAECTAEEAYTFTNGAALYASGSPFPNFELNGHTYKPGQGNNAYIFPGVALGTILFQIRHVDNDLFLLAAKKVASCVTEDSLKVGRVYPQLKEIREISIQIAVEMAKYCYKNGTANLYPQPEDLEKYVRAQVYNTEYEELINATYDWPEQDMRHGF 631
               SCOP domains d1llqb2 B:2-295 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                           d1llqb1 B:296-593 Mitochondrial NAD(P)-dependent malic enzyme                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1llqB04 B:294-478 NAD(P)-binding Rossmann-like Domain                                                                                                                                    ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------malic-1llqB03 B:103-286                                                                                                                                                                 ---------Malic_M-1llqB01 B:296-547                                                                                                                                                                                                                                   ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------malic-1llqB04 B:103-286                                                                                                                                                                 ---------Malic_M-1llqB02 B:296-547                                                                                                                                                                                                                                   ---------------------------------------------- Pfam domains (2)
         Sec.struct. author ................hhhhhhhhhhhh........hhhhhhh.....hhhhhhhhhhhhh...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh........eeee.hhhhhhhhhhhhh........eeeee..........hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee....hhhhhhh............hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhhhhhhh...hhhhhhh.eeeee..ee........hhhhhh..........hhhhhh.....eeee........hhhhhhhhhhhh...eeee...hhhhh..hhhhhhhh.....eeee......eee..eee..ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh...............hhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MALIC_ENZYMES    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1llq B   2 SVAHHEDVYSHNLPPMDEKEMALYKLYRPERVTPKKRSAELLKEPRLNKGMGFSLYERQYLGLHGLLPPAFMTQEQQAYRVITKLREQPNDLARYIQLDGLQDRNEKLFYRVVCDHVKELMPIVYTPTVGLACQNFGYIYRKPKGLYITINDNSVSKIYQILSNWHEEDVRAIVVTDGERILGLGDLGAYGIGIPVGKLALYVALGGVQPKWCLPVLLDVGTNNMDLLNDPFYIGLRHKRVRGKDYDTLLDNFMKACTKKYGQKTLIQFEDFANPNAFRLLDKYQDKYTMFNDDIQGTASVIVAGLLTCTRVTKKLVSQEKYLFFGAGAASTGIAEMIVHQMQNEGISKEEACNRIYLMDIDGLVTKNRKEMNPRHVQFAKDMPETTSILEVIRAARPGALIGASTVRGAFNEEVIRAMAEINERPIIFALSNPTSKAECTAEEAYTFTNGAALYASGSPFPNFELNGHTYKPGQGNNAYIFPGVALGTILFQIRHVDNDLFLLAAKKVASCVTEDSLKVGRVYPQLKEIREISIQIAVEMAKYCYKNGTANLYPQPEDLEKYVRAQVYNTEYEELINATYDWPEQDMRHGF 593
                                    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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MAOM_ASCSU | P27443)
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: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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008948    oxaloacetate decarboxylase activity    Catalysis of the reaction: oxaloacetate = pyruvate + CO2.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
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: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.
    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.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  1llq
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 Related Entries

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

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        MAOM_ASCSU | P27443: 1o0s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1LLQ)