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(-) Description

Title :  CRYSTAL STRUCTURE OF DELTA516-525 E201S HUMAN CYSTATHIONINE BETA-SYNTHASE WITH ADOMET
 
Authors :  J. Ereno-Orbea, T. Majtan, I. Oyenarte, J. P. Kraus, L. A. Martinez-Cru
Date :  16 Apr 14  (Deposition) - 24 Sep 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.58
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cbs Domain, Homocyteine, Cysteine Biosynthesis, Heme, Pyridoxal 5'- Phosphate, S-Adenosylmethionine, Transsulfuration Pathway, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Ereno-Orbea, T. Majtan, I. Oyenarte, J. P. Kraus, L. A. Martinez-Cruz
Structural Insight Into The Molecular Mechanism Of Allosteric Activation Of Human Cystathionine Beta-Synthase By S-Adenosylmethionine.
Proc. Natl. Acad. Sci. Usa V. 111 E3845 2014
PubMed-ID: 25197074  |  Reference-DOI: 10.1073/PNAS.1414545111

(-) Compounds

Molecule 1 - CYSTATHIONINE BETA-SYNTHASE
    Chains: A, B
    EC Number: 4.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CBS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-THIONASE, SERINE SULFHYDRASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:49 , SER A:50 , ARG A:51 , CYS A:52 , THR A:53 , TRP A:54 , PRO A:59 , GLU A:62 , SER A:63 , PRO A:64 , HIS A:65 , ALA A:226 , PRO A:229 , TYR A:233 , GLY A:263 , ARG A:266 , THR A:313 , ARG B:58 , HEM B:601binding site for residue HEM A 601
2AC2SOFTWARELYS A:119 , ASN A:149 , SER A:254 , GLY A:256 , THR A:257 , GLY A:258 , THR A:260 , GLU A:304 , GLY A:305 , ILE A:306 , SER A:349 , PRO A:375 , ASP A:376binding site for residue PLP A 602
3AC3SOFTWAREALA A:421 , PRO A:422 , LEU A:423 , GLY A:442 , PHE A:443 , ASP A:444 , GLN A:445 , VAL A:533 , THR A:535 , ILE A:537 , ASP A:538 , SAM B:603binding site for residue SAM A 603
4AC4SOFTWAREARG A:58 , HEM A:601 , PRO B:49 , SER B:50 , ARG B:51 , CYS B:52 , THR B:53 , TRP B:54 , PRO B:59 , GLU B:62 , SER B:63 , PRO B:64 , HIS B:65 , ARG B:224 , ALA B:226 , PRO B:229 , TYR B:233 , GLY B:263 , ARG B:266 , THR B:313binding site for residue HEM B 601
5AC5SOFTWARELYS B:119 , ASN B:149 , SER B:254 , GLY B:256 , THR B:257 , GLY B:258 , THR B:260 , GLU B:304 , GLY B:305 , ILE B:306 , SER B:349 , PRO B:375 , ASP B:376binding site for residue PLP B 602
6AC6SOFTWAREGLY A:442 , ASP A:444 , SAM A:603 , LEU B:423 , GLY B:442 , PHE B:443 , ASP B:444 , GLN B:445 , VAL B:533 , THR B:535 , ILE B:537 , ASP B:538binding site for residue SAM B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PCU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:289 -Pro A:290
2Glu B:289 -Pro B:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PCU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PCU)

(-) Exons   (0, 0)

(no "Exon" information available for 4PCU)

(-) 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:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................hhhhh............ee.hhhhhh....eee.hhhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh.eeee...........hhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhh....hhhhhhhh..........hhhhhhhhhhhh...........hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.......hhhhh............hhhhhhhhhhhh...............hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pcu A  43 WIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPARFDSPSSHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDLKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHEQMVFGVVTAIDLLNFVAA 545
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192|      204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       406       416       426       436       446       456       466       476       486       496       506       529       539      
                                                                                                                                                                               192|                                                                                                                                                                                                            402|                                                                                                          514|                 
                                                                                                                                                                                195                                                                                                                                                                                                             405                                                                                                           528                 


Chain B from PDB  Type:PROTEIN  Length:489
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhh............ee.hhhhhh....eee.hhhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee............hhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhh....hhhhhhhh............hhhhhh...........hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhh.......hhhhh............hhhhhhhhhhhh..eee..........eeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pcu B  43 WIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPSSHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHEQQRQMVFGVVTAIDLLNFVAAQE 547
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       408       418       428       438       448       458       468       478       488       498       508      |528       538         
                                                                                                                                                                                                                                                                                                                                                                                                401|                                                                                                        515|                     
                                                                                                                                                                                                                                                                                                                                                                                                 408                                                                                                         526
   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 4PCU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PCU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PCU)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBS_HUMAN | P35520: 1jbq 1m54 4coo 4l0d 4l27 4l28 4l3v 4uuu 5mms

(-) Related Entries Specified in the PDB File

4l0d 4l27 4l28 4l3v