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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCYL RADICAL ENZYME WITH BOUND SUBSTRATE
 
Authors :  B. M. Martins, M. Blaser, M. Feliks, G. M. Ullmann, T. Selmer
Date :  23 Feb 11  (Deposition) - 21 Sep 11  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Lyase, Radical Chemistry, Metalloenzyme, Iron-Sulfur Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Martins, M. Blaser, M. Feliks, G. M. Ullmann, W. Buckel, T. Selmer
Structural Basis For A Kolbe-Type Decarboxylation Catalyzed By A Glycyl Radical Enzyme.
J. Am. Chem. Soc. V. 133 14666 2011
PubMed-ID: 21823587  |  Reference-DOI: 10.1021/JA203344X

(-) Compounds

Molecule 1 - 4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
    Chains: A, C
    EC Number: 4.1.1.83
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: ROSETTA
    Expression System Vector: PASK-IBA
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM SCATOLOGENES
    Organism Taxid: 1548
    Other Details: GERMAN COLLECTION OF MICROORGANISMS
    Synonym: GLYCYL RADICAL ENZYME, 4-HYDROXYPHENYLACETATE DECARBOXYLASE GLYCYL RADICAL SUBUNIT, P-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT
 
Molecule 2 - 4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT
    Chains: B, D
    EC Number: 4.1.1.83
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: ROSETTA
    Expression System Vector: PASK-IBA
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM SCATOLOGENES
    Organism Taxid: 1548
    Other Details: GERMAN COLLECTION OF MICROORGANISMS
    Synonym: GLYCYL RADICAL ENZYME, P-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
14HP2Ligand/Ion4-HYDROXYPHENYLACETATE
2SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
14HP1Ligand/Ion4-HYDROXYPHENYLACETATE
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
14HP1Ligand/Ion4-HYDROXYPHENYLACETATE
2SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:3 , CYS B:6 , ASN B:8 , CYS B:19 , LEU B:21 , CYS B:36BINDING SITE FOR RESIDUE SF4 B 87
2AC2SOFTWARETRP A:58 , ARG A:61 , CYS B:45 , CYS B:48 , ASN B:50 , PHE B:51 , CYS B:62 , ALA B:77 , CYS B:80 , SER B:82 , TYR B:83BINDING SITE FOR RESIDUE SF4 B 88
3AC3SOFTWAREHIS D:3 , CYS D:6 , ASN D:8 , CYS D:19 , LEU D:21 , ALA D:35 , CYS D:36BINDING SITE FOR RESIDUE SF4 D 87
4AC4SOFTWARETRP C:58 , ARG C:61 , CYS D:45 , CYS D:48 , ASN D:50 , CYS D:62 , ALA D:77 , CYS D:80 , SER D:82 , TYR D:83BINDING SITE FOR RESIDUE SF4 D 88
5AC5SOFTWAREPHE A:214 , ARG A:223 , SER A:344 , GLY A:345 , VAL A:399 , LEU A:400 , PHE A:405 , GLY A:502 , CYS A:503 , GLU A:505 , GLY A:532 , HIS A:536 , PHE A:537 , GLU A:637 , ILE A:750BINDING SITE FOR RESIDUE 4HP A 1898
6AC6SOFTWAREPHE C:214 , ILE C:219 , ARG C:223 , SER C:344 , GLY C:345 , VAL C:399 , PHE C:405 , GLY C:502 , CYS C:503 , GLU C:505 , GLY C:532 , HIS C:536 , PHE C:537 , GLU C:637BINDING SITE FOR RESIDUE 4HP C 1898

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YAJ)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gln A:439 -Pro A:440
2Tyr A:468 -Pro A:469
3Pro A:614 -Asp A:615
4Gln C:439 -Pro C:440
5Tyr C:468 -Pro C:469
6Pro C:614 -Asp C:615

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YAJ)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFLPS51554 Pyruvate formate-lyase domain profile.HPDL_CLOSL35-770
 		  2A:35-770
C:35-770
2GLY_RADICAL_2PS51149 Glycine radical domain profile.HPDL_CLOSL778-897
 		  2A:778-897
C:778-897
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFLPS51554 Pyruvate formate-lyase domain profile.HPDL_CLOSL35-770
 		  1A:35-770
-
2GLY_RADICAL_2PS51149 Glycine radical domain profile.HPDL_CLOSL778-897
 		  1A:778-897
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFLPS51554 Pyruvate formate-lyase domain profile.HPDL_CLOSL35-770
 		  1-
C:35-770
2GLY_RADICAL_2PS51149 Glycine radical domain profile.HPDL_CLOSL778-897
 		  1-
C:778-897

(-) Exons   (0, 0)

(no "Exon" information available for 2YAJ)

(-) 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:869
 aligned with HPDL_CLOSL | Q38HX4 from UniProtKB/Swiss-Prot  Length:897

    Alignment length:869
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888         
           HPDL_CLOSL    29 DIPEAKESTQKLMDIYYTLKVTADMEAAYWYNRTWWENDGEVIEVRRAKAVAASLSHMTPTILPYEKLVMNKTKNVRGAFPFPWVCASFFNAQAEALMNEVDAPAENEADSVSVVGAGGGNVTESYGNVISIAKKFGMRKEEIPVLVKTSKPWEGISVEELSNKYSKMTPGYDQFKNIMESVICMFDSFAIPQGREVINYYMPLQYGFDGIIKLCDEKIAEVMGEAGDDGDFGMSRGYYYAAMKEITKGLSAWCENYSKRAKYLASIETDSEIKANYEKIEEVMGNIAHKKPANFWEAIQMTLCCHFGVVNEDPQSGLSIGRLGQVLQPFYEKDVEDGIMTDEEVIELLELYRIKITCIECFASAGVSGGVLSGNTFNNLSLGGQNYDGLSAVTPLEYLIVEAGMRNQTPQPTLSVLYDEKTPEDFLMKAASCTKLGLGYPAWMNNQTGMNFMMRNYGPEGMDLHDARAWCLGGCLESAPGCFLPLEYNGKVTMIPGGASPTCGTGVHFIGMPKVLELVLTNGLDKRTGKQVYPPHNKKLDSYETMVNQWKEYMELTTDVVNRCNNIQMDIWRKYNMPAVNSLLKPDCFKKGKHIGTMGARYNSCINFESCGTITFVNSLSSIKKNVFDDSKFTIEEMTDAMLNNFGFKTAYETEVFSPDFRESTDKSTKYEKIFAACVNAPKYGNADKYADEIFKAYHYYIYDMTHKFRSYYGKPLYLCQISVSTHGPQGFVTLATADGRLAGTTYSDGSVSAAAGTDKNGIYAIFESATVYDHSMHQNAQMNLKLHPTAVKGINGTRKLLDLVRAYMRKGGFHVQFNVVDSKTLRDAQLTPEKYRELMVRVAGFTQYWCEIGKPIQDEVIYRTEYDK 897
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....................ee.......hhhhhhhhhhhhh.......hhhhhh................eeee...eeee..hhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhh.....hhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhh..........eeee..........hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhh.hhhhhhh.eee...eee.eeeeeeee..eeeeeeee.......eeeeeehhhhhhhhhh..ee....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhh.hhhhh........eeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhh.........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........ee.....hhhhhhhh............................hhhhhhhhhh..hhhhh.....eeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh...eee....eee.hhhhhhhhhhhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PFL  PDB: A:35-770 UniProt: 35-770                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              -------GLY_RADICAL_2  PDB: A:778-897 UniProt: 778-897                                                                           PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yaj A  29 DIPEAKESTQKLMDIYYTLKVTADMEAAYWYNRTWWENDGEVIEVRRAKAVAASLSHMTPTILPYEKLVMNKTKNVRGAFPFPWVCASFFNAQAEALMNEVDAPAENEADSVSVVGAGGGNVTESYGNVISIAKKFGMRKEEIPVLVKTSKPWEGISVEELSNKYSKMTPGYDQFKNIMESVICMFDSFAIPQGREVINYYMPLQYGFDGIIKLCDEKIAEVMGEAGDDGDFGMSRGYYYAAMKEITKGLSAWCENYSKRAKYLASIETDSEIKANYEKIEEVMGNIAHKKPANFWEAIQMTLCCHFGVVNEDPQSGLSIGRLGQVLQPFYEKDVEDGIMTDEEVIELLELYRIKITCIECFASAGVSGGVLSGNTFNNLSLGGQNYDGLSAVTPLEYLIVEAGMRNQTPQPTLSVLYDEKTPEDFLMKAASCTKLGLGYPAWMNNQTGMNFMMRNYGPEGMDLHDARAWCLGGCLESAPGCFLPLEYNGKVTMIPGGASPTCGTGVHFIGMPKVLELVLTNGLDKRTGKQVYPPHNKKLDSYETMVNQWKEYMELTTDVVNRCNNIQMDIWRKYNMPAVNSLLKPDCFKKGKHIGTMGARYNSCINFESCGTITFVNSLSSIKKNVFDDSKFTIEEMTDAMLNNFGFKTAYETEVFSPDFRESTDKSTKYEKIFAACVNAPKYGNADKYADEIFKAYHYYIYDMTHKFRSYYGKPLYLCQISVSTHGPQGFVTLATADGRLAGTTYSDGSVSAAAGTDKNGIYAIFESATVYDHSMHQNAQMNLKLHPTAVKGINGTRKLLDLVRAYMRKGGFHVQFNVVDSKTLRDAQLTPEKYRELMVRVAGFTQYWCEIGKPIQDEVIYRTEYDK 897
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888         


Chain B from PDB  Type:PROTEIN  Length:86
 aligned with HPDS_CLOSL | Q38HX3 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           HPDS_CLOSL     1 MRHYDCKNYINLDCEKGLCALTKGMVPIDGEGSEACPNFKPAEKCGNCKNFCNPDKYGLGTCTGLEKENWAYATCGASACPSYKAE  86
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh...eee....eeee.....eee.................hhh...ee......eeee......eeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2yaj B   1 MRHYDCKNYINLDCEKGLCALTKGMVPIDGEGSEACPNFKPAEKCGNCKNFCNPDKYGLGTCTGLEKENWAYATCGASACPSYKAE  86
                                    10        20        30        40        50        60        70        80      


Chain C from PDB  Type:PROTEIN  Length:871
 aligned with HPDL_CLOSL | Q38HX4 from UniProtKB/Swiss-Prot  Length:897

    Alignment length:871
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896 
           HPDL_CLOSL    27 EADIPEAKESTQKLMDIYYTLKVTADMEAAYWYNRTWWENDGEVIEVRRAKAVAASLSHMTPTILPYEKLVMNKTKNVRGAFPFPWVCASFFNAQAEALMNEVDAPAENEADSVSVVGAGGGNVTESYGNVISIAKKFGMRKEEIPVLVKTSKPWEGISVEELSNKYSKMTPGYDQFKNIMESVICMFDSFAIPQGREVINYYMPLQYGFDGIIKLCDEKIAEVMGEAGDDGDFGMSRGYYYAAMKEITKGLSAWCENYSKRAKYLASIETDSEIKANYEKIEEVMGNIAHKKPANFWEAIQMTLCCHFGVVNEDPQSGLSIGRLGQVLQPFYEKDVEDGIMTDEEVIELLELYRIKITCIECFASAGVSGGVLSGNTFNNLSLGGQNYDGLSAVTPLEYLIVEAGMRNQTPQPTLSVLYDEKTPEDFLMKAASCTKLGLGYPAWMNNQTGMNFMMRNYGPEGMDLHDARAWCLGGCLESAPGCFLPLEYNGKVTMIPGGASPTCGTGVHFIGMPKVLELVLTNGLDKRTGKQVYPPHNKKLDSYETMVNQWKEYMELTTDVVNRCNNIQMDIWRKYNMPAVNSLLKPDCFKKGKHIGTMGARYNSCINFESCGTITFVNSLSSIKKNVFDDSKFTIEEMTDAMLNNFGFKTAYETEVFSPDFRESTDKSTKYEKIFAACVNAPKYGNADKYADEIFKAYHYYIYDMTHKFRSYYGKPLYLCQISVSTHGPQGFVTLATADGRLAGTTYSDGSVSAAAGTDKNGIYAIFESATVYDHSMHQNAQMNLKLHPTAVKGINGTRKLLDLVRAYMRKGGFHVQFNVVDSKTLRDAQLTPEKYRELMVRVAGFTQYWCEIGKPIQDEVIYRTEYDK 897
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh....ee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....................ee.......hhhhhhhhhhhhhh......hhhhhh................eeee...eeee..hhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhh.....hhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhh..........eeee..........hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhh.hhhhhh..eee...eee.eeeeeeee..eeeeeeee.......eeeeeehhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhh.hhhhh........eeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhh...........hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..........eee....hhhhhhhh............................hhhhhhhhhh..hhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh..eee....eee.hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PFL  PDB: C:35-770 UniProt: 35-770                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              -------GLY_RADICAL_2  PDB: C:778-897 UniProt: 778-897                                                                           PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yaj C  27 EADIPEAKESTQKLMDIYYTLKVTADMEAAYWYNRTWWENDGEVIEVRRAKAVAASLSHMTPTILPYEKLVMNKTKNVRGAFPFPWVCASFFNAQAEALMNEVDAPAENEADSVSVVGAGGGNVTESYGNVISIAKKFGMRKEEIPVLVKTSKPWEGISVEELSNKYSKMTPGYDQFKNIMESVICMFDSFAIPQGREVINYYMPLQYGFDGIIKLCDEKIAEVMGEAGDDGDFGMSRGYYYAAMKEITKGLSAWCENYSKRAKYLASIETDSEIKANYEKIEEVMGNIAHKKPANFWEAIQMTLCCHFGVVNEDPQSGLSIGRLGQVLQPFYEKDVEDGIMTDEEVIELLELYRIKITCIECFASAGVSGGVLSGNTFNNLSLGGQNYDGLSAVTPLEYLIVEAGMRNQTPQPTLSVLYDEKTPEDFLMKAASCTKLGLGYPAWMNNQTGMNFMMRNYGPEGMDLHDARAWCLGGCLESAPGCFLPLEYNGKVTMIPGGASPTCGTGVHFIGMPKVLELVLTNGLDKRTGKQVYPPHNKKLDSYETMVNQWKEYMELTTDVVNRCNNIQMDIWRKYNMPAVNSLLKPDCFKKGKHIGTMGARYNSCINFESCGTITFVNSLSSIKKNVFDDSKFTIEEMTDAMLNNFGFKTAYETEVFSPDFRESTDKSTKYEKIFAACVNAPKYGNADKYADEIFKAYHYYIYDMTHKFRSYYGKPLYLCQISVSTHGPQGFVTLATADGRLAGTTYSDGSVSAAAGTDKNGIYAIFESATVYDHSMHQNAQMNLKLHPTAVKGINGTRKLLDLVRAYMRKGGFHVQFNVVDSKTLRDAQLTPEKYRELMVRVAGFTQYWCEIGKPIQDEVIYRTEYDK 897
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896 


Chain D from PDB  Type:PROTEIN  Length:86
 aligned with HPDS_CLOSL | Q38HX3 from UniProtKB/Swiss-Prot  Length:86

    Alignment length:86
                                    10        20        30        40        50        60        70        80      
           HPDS_CLOSL     1 MRHYDCKNYINLDCEKGLCALTKGMVPIDGEGSEACPNFKPAEKCGNCKNFCNPDKYGLGTCTGLEKENWAYATCGASACPSYKAE  86
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh...eee....eeee.....eee.................hhh...ee......eeee......eeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2yaj D   1 MRHYDCKNYINLDCEKGLCALTKGMVPIDGEGSEACPNFKPAEKCGNCKNFCNPDKYGLGTCTGLEKENWAYATCGASACPSYKAE  86
                                    10        20        30        40        50        60        70        80
   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 2YAJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YAJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2YAJ)

(-) Gene Ontology  (7, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (HPDL_CLOSL | Q38HX4)
molecular function
    GO:0043722    4-hydroxyphenylacetate decarboxylase activity    Catalysis of the reaction: (4-hydroxyphenyl)acetate + H(+) = 4-cresol + CO(2).
    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.
biological process
    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.

Chain B,D   (HPDS_CLOSL | Q38HX3)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0043722    4-hydroxyphenylacetate decarboxylase activity    Catalysis of the reaction: (4-hydroxyphenyl)acetate + H(+) = 4-cresol + CO(2).
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 Visualization

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 Related Entries

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        HPDL_CLOSL | Q38HX4: 2y8n
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(-) Related Entries Specified in the PDB File

2y8n CRYSTAL STRUCTURE OF GLYCYL RADICAL ENZYME