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(-) Description

Title :  X-RAY STRUCTURE OF MALY FROM ESCHERICHIA COLI: A PYRIDOXAL-5'-PHOSPHATE-DEPENDENT ENZYME ACTING AS A MODULATOR IN MAL GENE EXPRESSION
 
Authors :  T. Clausen
Date :  23 Sep 99  (Deposition) - 12 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase Fold, Large Plp-Binding Domain, Small C-Terminal Domain, Open Alpha-Beta Structure. , Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Clausen, A. Schlegel, R. Peist, E. Schneider, C. Steegborn, Y. S. Chang, A. Haase, G. P. Bourenkov, H. D. Bartunik, W. Boos
X-Ray Structure Of Maly From Escherichia Coli: A Pyridoxal 5'-Phosphate-Dependent Enzyme Acting As A Modulator In Mal Gene Expression.
Embo J. V. 19 831 2000
PubMed-ID: 10698925  |  Reference-DOI: 10.1093/EMBOJ/19.5.831
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJR115
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:95 , VAL A:96 , ILE A:97 , CYS A:169 , ASN A:173 , ASP A:201 , ILE A:203 , HIS A:204 , LYS A:233 , HOH A:427 , HOH A:430 , TYR B:61BINDING SITE FOR RESIDUE PLP A 400
2AC2SOFTWARETYR A:61 , SER B:95 , VAL B:96 , ILE B:97 , CYS B:169 , ASN B:173 , ASP B:201 , ILE B:203 , HIS B:204 , LYS B:233BINDING SITE FOR RESIDUE PLP B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D2F)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:118 -Pro A:119
2Ser A:170 -Pro A:171
3Asn A:173 -Pro A:174
4Thr B:118 -Pro B:119
5Ser B:170 -Pro B:171
6Asn B:173 -Pro B:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D2F)

(-) Exons   (0, 0)

(no "Exon" information available for 1D2F)

(-) 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:361
 aligned with MALY_ECOLI | P23256 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:361
                                    39        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 
           MALY_ECOLI    30 LLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR 390
               SCOP domains d1d2fa_ A: Modulator in mal gene expression, MalY                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1d2fA01     1d2fA02 A:42-284 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                               1d2fA01 A:30-41,A:285-390 Aspartate Aminotransferase, domain 1                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..........hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhh..eeeeee.ee....ee.hhhhhhhhhh...eeeeeee............hhhhhhhhhhhhh..eeeee..............hhhhh....eeeee.hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhh.hhhhhhhhhhhh..ee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d2f A  30 LLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR 390
                                    39        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 


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with MALY_ECOLI | P23256 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    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         
           MALY_ECOLI     2 FDFSKVVDRHGTWCTQWDYVADRFGTADLLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR 390
               SCOP domains d1d2fb_                      B: Modulator in mal gene expression, MalY                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1d2fB01                      B:2-41,B:281d2fB02 B:42-284 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                               1d2fB01 B:2-41,B:285-389 Aspartate Aminotransferase, domain 1                                            - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......---------------------.ee..........hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh....hhh.eeee.hhhhhhhhhhhhhh....eeeeee...hhhhhhhhhh..eeeeee.eee..eee.hhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh..eeeee..............hhhhh....eeeee.hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.hhhh.hhhhhhhhhhhh..ee.ee.hhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d2f B   2 FDFSKVV---------------------LLPFTISDMDFATAPCIIEALNQRLMHGVFGYSRWKNDEFLAAIAHWFSTQHYTAIDSQTVVYGPSVIYMVSELIRQWSETGEGVVIHTPAYDAFYKAIEGNQRTVMPVALEKQADGWFCDMGKLEAVLAKPECKIMLLCSPQNPTGKVWTCDELEIMADLCERHGVRVISDEIHMDMVWGEQPHIPWSNVARGDWALLTSGSKSFNIPALTGAYGIIENSSSRDAYLSALKGRDGLSSPSVLALTAHIAAYQQGAPWLDALRIYLKDNLTYIADKMNAAFPELNWQIPQSTYLAWLDLRPLNIDDNALQKALIEQEKVAIMPGYTYGEEGRGFVRLNAGCPRSKLEKGVAGLINAIRAVR 390
                                  |  -         -        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         
                                  8                    30
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D2F)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MALY_ECOLI | P23256)
molecular function
    GO:0080146    L-cysteine desulfhydrase activity    Catalysis of the reaction: L-cysteine + H2O = ammonia + pyruvate + hydrogen sulfide + H+.
    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:0004121    cystathionine beta-lyase activity    Catalysis of the reaction: cystathionine + H2O = L-homocysteine + NH3 + pyruvate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
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:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1ajs 1AJS IS THE CLOSEST STRUCTURAL HOMOLOGUE OF MALY.
1cl1 1CL1 IS AS MALY A PLP-DEPENDENT BETA-CYSTATHIONASE.