Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF L-METHIONINE ALPHA-, GAMMA-LYASE
 
Authors :  T. W. Allen, V. Sridhar, G. S. Prasad, Q. Han, M. Xu, Y. Tan, R. M. Hoffman, S. Ramaswamy
Date :  28 May 03  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  

PubMed: search

(-) Compounds

Molecule 1 - METHIONINE GAMMA-LYASE
    Chains: A, B, C, D
    EC Number: 4.4.1.11
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: L-METHIONINASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1PEG11Ligand/IonDI(HYDROXYETHYL)ETHER
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SO44Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR C:114 , LYS C:211 , VAL C:339 , SER C:340 , GLN C:349 , ARG C:375 , HOH C:1284 , HOH C:1285BINDING SITE FOR RESIDUE SO4 C 1146
02AC2SOFTWARETYR A:114 , ASN A:161 , LYS A:211 , VAL A:339 , SER A:340 , ARG A:375 , HOH A:1495 , HOH A:1496BINDING SITE FOR RESIDUE SO4 A 1124
03AC3SOFTWARETYR B:114 , LYS B:211 , VAL B:339 , SER B:340 , LEU B:341 , GLN B:349 , ARG B:375 , PLP B:1799BINDING SITE FOR RESIDUE SO4 B 1138
04AC4SOFTWARETYR D:114 , LYS D:211 , VAL D:339 , SER D:340 , GLN D:349 , ARG D:375BINDING SITE FOR RESIDUE SO4 D 1147
05AC5SOFTWARESER A:88 , GLY A:89 , MET A:90 , ILE A:93 , TYR A:114 , ASP A:186 , SER A:208 , THR A:210 , LYS A:211 , HOH A:1495 , TYR C:59 , ARG C:61BINDING SITE FOR RESIDUE PLP A 1399
06AC6SOFTWARESER B:88 , GLY B:89 , MET B:90 , TYR B:114 , ASP B:186 , TYR B:189 , SER B:208 , THR B:210 , LYS B:211 , LEU B:341 , SO4 B:1138 , TYR D:59 , ARG D:61BINDING SITE FOR RESIDUE PLP B 1799
07AC7SOFTWARETYR A:59 , ARG A:61 , SER C:88 , GLY C:89 , MET C:90 , TYR C:114 , ASP C:186 , TYR C:189 , SER C:208 , THR C:210 , LYS C:211 , HOH C:1284BINDING SITE FOR RESIDUE PLP C 1199
08AC8SOFTWARETYR B:59 , ARG B:61 , SER D:88 , GLY D:89 , MET D:90 , TYR D:114 , ASP D:186 , THR D:188 , TYR D:189 , SER D:208 , THR D:210 , LYS D:211 , LEU D:341BINDING SITE FOR RESIDUE PLP D 1599
09AC9SOFTWARESER A:4 , LYS A:6 , PEG A:1002 , HOH A:1404 , ASP D:385BINDING SITE FOR RESIDUE PEG A 1001
10BC1SOFTWAREPRO A:8 , THR A:12 , ARG A:13 , HIS A:17 , PEG A:1001 , PEG A:1003 , HOH A:1404 , HOH A:1499BINDING SITE FOR RESIDUE PEG A 1002
11BC2SOFTWAREHIS A:16 , TYR A:19 , PEG A:1002BINDING SITE FOR RESIDUE PEG A 1003
12BC3SOFTWAREHIS A:24 , TYR A:33 , HIS A:57 , GLY B:25BINDING SITE FOR RESIDUE PEG A 1004
13BC4SOFTWAREGLY A:25 , HIS B:24BINDING SITE FOR RESIDUE PEG A 1005
14BC5SOFTWAREGLY B:18 , TYR B:19 , HIS B:24 , PRO B:30 , PRO B:31 , VAL B:32 , PRO B:65 , THR B:66BINDING SITE FOR RESIDUE PEG B 1006
15BC6SOFTWAREALA A:295 , SER A:296 , PHE A:297 , PRO A:298 , TYR A:300 , THR A:301 , ALA C:271 , GLN C:274 , VAL C:275 , GLU C:278 , HOH C:1281BINDING SITE FOR RESIDUE PEG A 1007
16BC7SOFTWAREGLY A:110 , ASN A:111 , THR A:112 , LEU A:113 , VAL A:135 , ASP A:136 , MET A:137 , PHE A:156 , GLU A:157 , ALA A:160 , HIS A:165 , HOH A:1431BINDING SITE FOR RESIDUE PEG A 1008
17BC8SOFTWAREALA B:11 , ASN B:263 , ARG C:268 , ASN C:272 , LEU C:380 , GLU C:381 , ASP C:382 , ILE C:383 , HOH C:1265BINDING SITE FOR RESIDUE PEG C 1009
18BC9SOFTWAREPRO B:8 , HIS B:17BINDING SITE FOR RESIDUE PEG B 1010
19CC1SOFTWAREHIS B:16 , ASP B:20 , GLN C:333 , LEU C:334 , SER C:336 , HOH C:1216BINDING SITE FOR RESIDUE PEG C 1012

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PG8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:158 -Pro A:159
2Ser B:158 -Pro B:159
3Ser C:158 -Pro C:159
4Ser D:158 -Pro D:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PG8)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYS_MET_METAB_PPPS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.MEGL_PSEPU203-217
 
 
 		  4A:203-217
B:203-217
C:203-217
D:203-217

(-) Exons   (0, 0)

(no "Exon" information available for 1PG8)

(-) 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:398
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    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        
           MEGL_PSEPU     1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1pg8a_ A: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------1pg8A01 A:8-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1pg8A02 A:263-396 Aspartate Aminotransferase, domain 1                                                                                -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh..hhhhhh................hhhhhhhhhhh...........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee..hhhhhhhhhhh....ee.........eeehhhhh.....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pg8 A   1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    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        


Chain B from PDB  Type:PROTEIN  Length:398
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    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        
           MEGL_PSEPU     1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1pg8b_ B: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------1pg8B01 B:8-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1pg8B02 B:263-396 Aspartate Aminotransferase, domain 1                                                                                -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh..hhhhh.................hhhhhhhhhhh...........hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeeeee..........hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhh..eeeee.............eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eeehhhhh....hhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pg8 B   1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    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        


Chain C from PDB  Type:PROTEIN  Length:398
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    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        
           MEGL_PSEPU     1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1pg8c_ C: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------1pg8C01 C:8-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1pg8C02 C:263-396 Aspartate Aminotransferase, domain 1                                                                                -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhh..hhhhhh................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh.eeee....hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee...hhhhhh........eeeee.............eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eeehhhhh.....hhhhhhhh.....eeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pg8 C   1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    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        


Chain D from PDB  Type:PROTEIN  Length:398
 aligned with MEGL_PSEPU | P13254 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    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        
           MEGL_PSEPU     1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
               SCOP domains d1pg8d_ D: Methionine gamma-lyase, MGL                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------1pg8D01 D:8-262 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                            1pg8D02 D:263-396 Aspartate Aminotransferase, domain 1                                                                                -- CATH domains
           Pfam domains (1) ----------Cys_Met_Meta_PP-1pg8D01 D:11-395                                                                                                                                                                                                                                                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) ----------Cys_Met_Meta_PP-1pg8D02 D:11-395                                                                                                                                                                                                                                                                                                                                                                 --- Pfam domains (2)
           Pfam domains (3) ----------Cys_Met_Meta_PP-1pg8D03 D:11-395                                                                                                                                                                                                                                                                                                                                                                 --- Pfam domains (3)
           Pfam domains (4) ----------Cys_Met_Meta_PP-1pg8D04 D:11-395                                                                                                                                                                                                                                                                                                                                                                 --- Pfam domains (4)
         Sec.struct. author ........hhhhhhhhh..hhhhhh................hhhhhhhhhh............hhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh.eeeee.........hhhhhh..eeeee.............eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhh.....eeeeee.hhhhhhhhhhhhh...ee.........eee..........hhhhhhhh.....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYS_MET_METAB_P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pg8 D   1 MHGSNKLPGFATRAIHHGYDPQDHGGALVPPVYQTATFTFPTVEYGAACFAGEQAGHFYSRISNPTLNLLEARMASLEGGEAGLALASGMGAITSTLWTLLRPGDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQALEAAMTPATRVIYFESPANPNMHMADIAGVAKIARKHGATVVVDNTYCTPYLQRPLELGADLVVHSATKYLSGHGDITAGIVVGSQALVDRIRLQGLKDMTGAVLSPHDAALLMRGIKTLNLRMDRHCANAQVLAEFLARQPQVELIHYPGLASFPQYTLARQQMSQPGGMIAFELKGGIGAGRRFMNALQLFSRAVSLGDAESLAQHPASMTHSSYTPEERAHYGISEGLVRLSVGLEDIDDLLADVQQALKASA 398
                                    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
   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, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MEGL_PSEPU | P13254)
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:0047982    homocysteine desulfhydrase activity    Catalysis of the reaction: L-homocysteine + H2O = sulfide + NH3 + 2-oxobutanoate.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:158 - Pro A:159   [ RasMol ]  
    Ser B:158 - Pro B:159   [ RasMol ]  
    Ser C:158 - Pro C:159   [ RasMol ]  
    Ser D:158 - Pro D:159   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pg8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MEGL_PSEPU | P13254
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.4.1.11
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MEGL_PSEPU | P13254
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MEGL_PSEPU | P13254: 1gc0 1gc2 1ukj 2o7c 3vk2 3vk3 3vk4 5x2v 5x2w 5x2x 5x2y 5x2z 5x30

(-) Related Entries Specified in the PDB File

1pff L-HOMOCYSTEINE ALPHA-, GAMMA-LYASE