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(-) Description

Title :  CRYSTAL STRUCTURE OF LUPINUS LUTEUS S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE IN COMPLEX WITH ADENINE
 
Authors :  K. Brzezinski, M. Jaskolski
Date :  28 Aug 10  (Deposition) - 31 Aug 11  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Plant Protein, Enzyme-Inhibitor Complex, Nad Cofactor, Regulation Of Sam-Dependent Methylation Reactions, Hydrolase-Hydrolase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Brzezinski, Z. Dauter, M. Jaskolski
High-Resolution Structures Of Complexes Of Plant S-Adenosyl-L-Homocysteine Hydrolase (Lupinus Luteus).
Acta Crystallogr. , Sect. D V. 68 218 2012
PubMed-ID: 22349223  |  Reference-DOI: 10.1107/S0907444911055090
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOSYLHOMOCYSTEINASE
    ChainsA, B
    EC Number3.3.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21-CODONPLUS (DE3)-RIPL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSAHH, SHH, SHH-1
    Organism CommonEUROPEAN YELLOW LUPIN
    Organism ScientificLUPINUS LUTEUS
    Organism Taxid3873
    SynonymADOHCYASE, SAHASE, S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2NA2Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1ADE4Ligand/IonADENINE
2NA-1Ligand/IonSODIUM ION
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1ADE2Ligand/IonADENINE
2NA-1Ligand/IonSODIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4TRS3Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:206 , THR A:207 , THR A:208 , ASN A:240 , GLY A:269 , GLY A:271 , ASP A:272 , VAL A:273 , THR A:291 , GLU A:292 , ILE A:293 , ASP A:294 , CYS A:297 , THR A:324 , THR A:325 , GLY A:326 , ASN A:327 , ILE A:330 , ILE A:348 , GLY A:349 , HIS A:350 , LEU A:395 , ASN A:397 , HIS A:404 , ADE A:506 , HOH A:512 , HOH A:555 , HOH A:576 , HOH A:591 , HOH A:655 , HOH A:696 , HOH A:715 , GLN B:466 , LYS B:479 , TYR B:483BINDING SITE FOR RESIDUE NAD A 501
2AC2SOFTWARETHR A:460 , VAL A:474 , GLU A:475 , TYR A:478 , HOH A:643 , HOH A:719 , HOH B:1073BINDING SITE FOR RESIDUE TRS A 505
3AC3SOFTWAREHIS A:62 , THR A:64 , GLN A:66 , THR A:67 , THR A:402 , GLY A:403 , HIS A:404 , MET A:409 , PHE A:413 , NAD A:501 , HOH A:754 , HOH A:937BINDING SITE FOR RESIDUE ADE A 506
4AC4SOFTWARETHR A:402 , GLY A:403 , HIS A:404 , HOH A:537 , HOH A:653BINDING SITE FOR RESIDUE NA A 509
5AC5SOFTWARELYS A:479 , TYR A:483 , THR B:206 , THR B:207 , THR B:208 , ASP B:239 , ASN B:240 , GLY B:269 , GLY B:271 , ASP B:272 , VAL B:273 , THR B:291 , GLU B:292 , ILE B:293 , ASP B:294 , CYS B:297 , THR B:324 , THR B:325 , GLY B:326 , ASN B:327 , ILE B:330 , ILE B:348 , GLY B:349 , HIS B:350 , LEU B:395 , ASN B:397 , HIS B:404 , HOH B:487 , ADE B:507 , HOH B:536 , HOH B:553 , HOH B:613 , HOH B:627 , HOH B:656 , HOH B:702BINDING SITE FOR RESIDUE NAD B 502
6AC6SOFTWAREHOH A:1072 , VAL B:474 , GLU B:475 , TYR B:478 , HOH B:530 , HOH B:718 , HOH B:1102BINDING SITE FOR RESIDUE TRS B 503
7AC7SOFTWAREGLU B:361 , VAL B:366 , LYS B:367 , ARG B:368 , TRP B:378 , HOH B:568 , HOH B:682 , HOH B:1221BINDING SITE FOR RESIDUE TRS B 504
8AC8SOFTWARETHR B:64 , GLN B:66 , THR B:67 , THR B:402 , HIS B:404 , MET B:409 , PHE B:413 , NAD B:502 , HOH B:738 , HOH B:755BINDING SITE FOR RESIDUE ADE B 507
9AC9SOFTWARETHR B:402 , GLY B:403 , HIS B:404 , HOH B:856 , HOH B:1103BINDING SITE FOR RESIDUE NA B 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ONE)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:132 -Pro A:133
2Gly A:476 -Pro A:477
3Gly B:132 -Pro B:133
4Gly B:476 -Pro B:477

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ONE)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOHCYASE_1PS00738 S-adenosyl-L-homocysteine hydrolase signature 1.SAHH_LUPLU85-99
 
  2A:85-99
B:85-99
2ADOHCYASE_2PS00739 S-adenosyl-L-homocysteine hydrolase signature 2.SAHH_LUPLU262-279
 
  2A:262-279
B:262-279
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOHCYASE_1PS00738 S-adenosyl-L-homocysteine hydrolase signature 1.SAHH_LUPLU85-99
 
  4A:85-99
B:85-99
2ADOHCYASE_2PS00739 S-adenosyl-L-homocysteine hydrolase signature 2.SAHH_LUPLU262-279
 
  4A:262-279
B:262-279
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADOHCYASE_1PS00738 S-adenosyl-L-homocysteine hydrolase signature 1.SAHH_LUPLU85-99
 
  2A:85-99
B:85-99
2ADOHCYASE_2PS00739 S-adenosyl-L-homocysteine hydrolase signature 2.SAHH_LUPLU262-279
 
  2A:262-279
B:262-279

(-) Exons   (0, 0)

(no "Exon" information available for 3ONE)

(-) 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:487
 aligned with SAHH_LUPLU | Q9SP37 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:487
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        18        28        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       
           SAHH_LUPLU     - --MALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhh.eeee.hhhhhhhhhhhhhh......eee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhh....eeee........hhhhhh.....eeeee...hhhhhhhhhhhh....eeeeee..eeeee......eeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........ee..hhhhhhhhhhhhhhhhh......hhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------ADOHCYASE_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------ADOHCYASE_2       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3one A  -1 SHMALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
                                     8        18        28        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       

Chain B from PDB  Type:PROTEIN  Length:488
 aligned with SAHH_LUPLU | Q9SP37 from UniProtKB/Swiss-Prot  Length:485

    Alignment length:488
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        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       407       417       427       437       447       457       467       477        
           SAHH_LUPLU     - ---MALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee.....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee....hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.eeee.hhhhhhhhhhhhhh......eee...hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee.hhhhhh....eeee........hhhhhh.....eeeee...hhhhhhhhhhhh....eeeeee..eeeeee....eeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........ee..hhhhhhhhhhhhhhhhh......hhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------ADOHCYASE_1    ------------------------------------------------------------------------------------------------------------------------------------------------------------------ADOHCYASE_2       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3one B  -2 GSHMALLVEKTTSGREYKVKDMSQADFGRLEIELAEVEMPGLMASRSEFGPSQPFKGAKITGSLHMTIQTAVLIETLTALGAEVRWCSCNIFSTQDHAAAAIARDSAAVFAWKGETLQEYWWCTERALDWGPGGGPDLIVDDGGDTTLLIHEGVKAEEIYEKSGQFPDPDSTDNAEFKIVLSIIKEGLKTDPKRYHKMKDRVVGVSEETTTGVKRLYQMQANGTLLFPAINVNDSVTKSKFDNLYGCRHSLPDGLMRATDVMIAGKVAVVAGYGDVGKGCAAALKQAGARVIVTEIDPICALQATMEGLQVLTLEDVVSEADIFVTTTGNKDIIMLDHMKKMKNNAIVCNIGHFDNEIDMLGLETHPGVKRITIKPQTDRWVFPETNTGIIILAEGRLMNLGCATGHPSFVMSCSFTNQVIAQLELWNEKSSGKYEKKVYVLPKHLDEKVAALHLEKLGAKLTKLSKDQADYISVPVEGPYKPFHYRY 485
                                     7        17        27        37        47        57        67        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       407       417       427       437       447       457       467       477        

   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 3ONE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ONE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ONE)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SAHH_LUPLU | Q9SP37)
molecular function
    GO:0004013    adenosylhomocysteinase activity    Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenosine + L-homocysteine.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SAHH_LUPLU | Q9SP373ond 3onf

(-) Related Entries Specified in the PDB File

1a7a STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH
1b3r RAT LIVER S-ADENOSYLHOMOCYSTEINE HYDROLASE
1v8b CRYSTAL STRUCTURE OF S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE FROM THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM
3ce6 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS S-ADENOSYL- L-HOMOCYSTEINE HYDROLASE IN TERNARY COMPLEX WITH NAD AND ADENOSINE
3ond CRYSTAL STRUCTURE OF LUPINUS LUTEUS S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE IN COMPLEX WITH ADENOSINE
3onf CRYSTAL STRUCTURE OF LUPINUS LUTEUS S-ADENOSYL-L- HOMOCYSTEINE HYDROLASE IN COMPLEX WITH CORDYCEPIN