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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMOCYSTEINE ALPHA-, GAMMA-LYASE AT 1.8 ANGSTROMS
 
Authors :  T. W. Allen, V. Sridhar, S. G. Prasad, Q. Han, M. Xu, Y. Tan, R. M. Hoffman, S. Ramaswamy
Date :  26 May 03  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Gamma-Lyase, Homocysteine, Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  

PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Chains: A, B
    EC Number: 4.4.1.11
    Organism Scientific: TRICHOMONAS VAGINALIS
    Organism Taxid: 5722

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1EDO21Ligand/Ion1,2-ETHANEDIOL
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 48)
No.NameCountTypeFull Name
1EDO42Ligand/Ion1,2-ETHANEDIOL
2PEG6Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:101 , GLU A:128 , PEG A:1502BINDING SITE FOR RESIDUE EDO A 1001
02AC2SOFTWAREALA A:66 , HOH A:1625BINDING SITE FOR RESIDUE EDO A 1002
03AC3SOFTWAREEDO A:1008 , ASP B:197BINDING SITE FOR RESIDUE EDO A 1003
04AC4SOFTWAREHIS A:143 , ASP A:318BINDING SITE FOR RESIDUE EDO A 1004
05AC5SOFTWARELEU A:144 , PRO A:146 , HIS A:279 , LYS A:285 , EDO A:1006 , EDO A:1007 , HOH A:1528 , HOH A:1540BINDING SITE FOR RESIDUE EDO A 1005
06AC6SOFTWAREGLU A:280 , LYS A:282 , EDO A:1005 , EDO A:1007BINDING SITE FOR RESIDUE EDO A 1006
07AC7SOFTWARELEU A:278 , HIS A:279 , HIS A:281 , VAL A:284 , LYS A:285 , VAL A:287 , EDO A:1005 , EDO A:1006BINDING SITE FOR RESIDUE EDO A 1007
08AC8SOFTWAREEDO A:1003 , PEG A:1502 , GLU B:167 , LEU B:198BINDING SITE FOR RESIDUE EDO A 1008
09AC9SOFTWAREASP B:108 , CYS B:109 , ALA B:365BINDING SITE FOR RESIDUE EDO B 1009
10BC1SOFTWAREHIS B:279 , GLU B:280 , GLN B:382 , ASP B:386BINDING SITE FOR RESIDUE EDO B 1010
11BC2SOFTWARELEU B:74 , HIS B:76 , PRO B:190 , GLU B:321 , HOH B:1618BINDING SITE FOR RESIDUE EDO B 1011
12BC3SOFTWAREGLU A:280 , ASP B:318BINDING SITE FOR RESIDUE EDO B 1012
13BC4SOFTWAREGLN A:235 , EDO A:1015 , HOH B:1567BINDING SITE FOR RESIDUE EDO A 1013
14BC5SOFTWARELEU A:74 , HOH A:1510 , HOH A:1544 , GLU B:379 , ASN B:380 , ASP B:383BINDING SITE FOR RESIDUE EDO A 1014
15BC6SOFTWARELYS A:231 , EDO A:1013 , GLN B:176 , HOH B:1567BINDING SITE FOR RESIDUE EDO A 1015
16BC7SOFTWARELYS A:231 , HOH A:1671BINDING SITE FOR RESIDUE EDO A 1016
17BC8SOFTWAREARG A:123 , GLU A:128 , VAL A:129 , HOH A:1627BINDING SITE FOR RESIDUE EDO A 1017
18BC9SOFTWARECYS A:109 , THR A:160 , LYS A:175 , GLY A:366BINDING SITE FOR RESIDUE EDO A 1018
19CC1SOFTWARETHR A:160 , LYS A:162 , LYS A:175 , PRO A:296 , HOH A:1512 , HOH A:1521 , HOH A:1533 , HOH A:1570BINDING SITE FOR RESIDUE EDO A 1019
20CC2SOFTWAREILE A:90 , TYR A:111 , ASP A:184BINDING SITE FOR RESIDUE EDO A 1020
21CC3SOFTWAREALA A:336 , VAL A:337 , SER A:338BINDING SITE FOR RESIDUE EDO A 1021
22CC4SOFTWARELYS A:273 , LEU B:192 , LYS B:302 , LYS B:303 , GLN B:304 , MET B:305 , LYS B:306 , HOH B:1545BINDING SITE FOR RESIDUE PEG B 1500
23CC5SOFTWAREALA A:84 , VAL A:218 , ILE A:244 , ILE A:245 , SER A:246 , HOH A:1568 , ALA B:84 , VAL B:218 , ILE B:244 , ILE B:245 , SER B:246 , ASP B:249 , HOH B:1543BINDING SITE FOR RESIDUE PEG B 1501
24CC6SOFTWAREARG A:149 , EDO A:1001 , EDO A:1008 , HOH A:1691 , ARG B:174BINDING SITE FOR RESIDUE PEG A 1502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:155 -Pro A:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PFF)

(-) 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:331
 aligned with O15565_TRIVA | O15565 from UniProtKB/TrEMBL  Length:398

    Alignment length:331
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397 
         O15565_TRIVA    68 SALEGKIAKLEHAEACAATASGMGAIAASVWTFLKAGDHLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAVPGNIEKHLKPNTRIVYFETPANPTLKVIDIEDAVKQARKQKDILVIVDNTFASPILTNPLDLGVDIVVHSATKYINGHTDVVAGLVCSRADIIAKVKSQGIKDITGAIISPHDAWLITRGTLTLDMRVKRAAENAQKVAEFLHEHKAVKKVYYPGLPDHPGHEIAKKQMKMFGSMIAFDVDGLEKAKKVLDNCHVVSLAVSLGGPESLIQHPASMTHAGVPKEEREAAGLTDNLIRLSVGCENVQDIIDDLKQALDLVL 398
               SCOP domains d1pffa_ A: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhh....eeeeeee..........hhhhhhhhhh.....eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhh.....eeeee..hhhhhhhhhhh....ee.........eeehhhhhh....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pff A  65 SALEGKIAKLEHAEACAATASGMGAIAASVWTFLKAGDHLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAVPGNIEKHLKPNTRIVYFETPANPTLKVIDIEDAVKQARKQKDILVIVDNTFASPILTNPLDLGVDIVVHSATKYINGHTDVVAGLVCSRADIIAKVKSQGIKDITGAIISPHDAWLITRGTLTLDMRVKRAAENAQKVAEFLHEHKAVKKVYYPGLPDHPGHEIAKKQMKMFGSMIAFDVDGLEKAKKVLDNCHVVSLAVSLGGPESLIQHPASMTHAGVPKEEREAAGLTDNLIRLSVGCENVQDIIDDLKQALDLVL 396
                                    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 ||    325       335       345       355       365       375       385       395 
                                                                                                                                                                                                                                                                                     316|                                                                              
                                                                                                                                                                                                                                                                                      318                                                                              


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with O15565_TRIVA | O15565 from UniProtKB/TrEMBL  Length:398

    Alignment length:331
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397 
         O15565_TRIVA    68 SALEGKIAKLEHAEACAATASGMGAIAASVWTFLKAGDHLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAVPGNIEKHLKPNTRIVYFETPANPTLKVIDIEDAVKQARKQKDILVIVDNTFASPILTNPLDLGVDIVVHSATKYINGHTDVVAGLVCSRADIIAKVKSQGIKDITGAIISPHDAWLITRGTLTLDMRVKRAAENAQKVAEFLHEHKAVKKVYYPGLPDHPGHEIAKKQMKMFGSMIAFDVDGLEKAKKVLDNCHVVSLAVSLGGPESLIQHPASMTHAGVPKEEREAAGLTDNLIRLSVGCENVQDIIDDLKQALDLVL 398
               SCOP domains d1pffb_ B: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Cys_Met_Meta_PP-1pffB01 B:65-393                                                                                                                                                                                                                                                                                                        --- Pfam domains (1)
           Pfam domains (2) Cys_Met_Meta_PP-1pffB02 B:65-393                                                                                                                                                                                                                                                                                                        --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh...eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee.....hhhhhhh...eeeeeee..........hhhhhhhhhh.....eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhh.....eeeee..hhhhhhhhhhh....ee.........eeehhhhhh....hhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pff B  65 SALEGKIAKLEHAEACAATASGMGAIAASVWTFLKAGDHLISDDCLYGCTHALFEHQLRKFGVEVDFIDMAVPGNIEKHLKPNTRIVYFETPANPTLKVIDIEDAVKQARKQKDILVIVDNTFASPILTNPLDLGVDIVVHSATKYINGHTDVVAGLVCSRADIIAKVKSQGIKDITGAIISPHDAWLITRGTLTLDMRVKRAAENAQKVAEFLHEHKAVKKVYYPGLPDHPGHEIAKKQMKMFGSMIAFDVDGLEKAKKVLDNCHVVSLAVSLGGPESLIQHPASMTHAGVPKEEREAAGLTDNLIRLSVGCENVQDIIDDLKQALDLVL 396
                                    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 ||    325       335       345       355       365       375       385       395 
                                                                                                                                                                                                                                                                                     316|                                                                              
                                                                                                                                                                                                                                                                                      318
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PFF)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O15565_TRIVA | O15565)
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: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:0018826    methionine gamma-lyase activity    Catalysis of the reaction: L-methionine = methanethiol + NH3 + 2-oxobutanoate.
    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.

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1pg8 CRYSTAL STRUCTURE OF L-METHIONINE ALPHA-, GAMMA-LYASE