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(-) Description

Title :  CRYSTAL STRUCTURE OF DELTA1-39 AND DELTA516-525 HUMAN CYSTATHIONINE BETA-SYNTHASE D444N MUTANT CONTAINING C-TERMINAL 6XHIS TAG
 
Authors :  J. Ereno, T. Majtan, I. Oyenarte, J. P. Kraus, L. A. Martinez
Date :  04 Jun 13  (Deposition) - 18 Sep 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.39
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
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 Basis Of Regulation And Oligomerization Of Human Cystathionine Beta-Synthase, The Central Enzyme Of Transsulfuration.
Proc. Natl. Acad. Sci. Usa V. 110 E3790 2013
PubMed-ID: 24043838  |  Reference-DOI: 10.1073/PNAS.1313683110

(-) Compounds

Molecule 1 - CYSTATHIONINE BETA-SYNTHASE
    Chains: B, D, A, C
    EC Number: 4.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) GOLD
    Expression System Taxid: 469008
    Gene: CBS
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-THIONASE, SERINE SULFHYDRASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:119 , SER B:147 , ASN B:149 , VAL B:255 , GLY B:256 , THR B:257 , GLY B:258 , GLY B:259 , THR B:260 , ILE B:306 , SER B:349 , PRO B:375 , ASP B:376 , TYR B:381BINDING SITE FOR RESIDUE PLP B 601
2AC2SOFTWAREARG B:51 , CYS B:52 , THR B:53 , TRP B:54 , ARG B:58 , GLU B:62 , SER B:63 , PRO B:64 , HIS B:65 , ARG B:224 , ALA B:226 , PRO B:229 , LEU B:230 , TYR B:233 , ARG B:266 , VAL B:314BINDING SITE FOR RESIDUE HEM B 602
3AC3SOFTWARELYS D:119 , ASN D:149 , SER D:254 , VAL D:255 , GLY D:256 , THR D:257 , GLY D:258 , GLY D:259 , THR D:260 , GLY D:305 , ILE D:306 , SER D:349 , PRO D:375 , ASP D:376 , TYR D:381BINDING SITE FOR RESIDUE PLP D 601
4AC4SOFTWAREPRO D:49 , SER D:50 , ARG D:51 , CYS D:52 , THR D:53 , TRP D:54 , ARG D:58 , PRO D:59 , GLU D:62 , SER D:63 , PRO D:64 , HIS D:65 , ARG D:224 , ALA D:226 , PRO D:229 , TYR D:233 , ARG D:266 , THR D:313BINDING SITE FOR RESIDUE HEM D 602
5AC5SOFTWARELYS A:119 , ASN A:149 , SER A:254 , VAL A:255 , GLY A:256 , THR A:257 , GLY A:258 , GLY A:259 , THR A:260 , GLU A:304 , ILE A:306 , SER A:349 , PRO A:375 , ASP A:376 , TYR A:381BINDING SITE FOR RESIDUE PLP A 601
6AC6SOFTWARESER A:50 , ARG A:51 , CYS A:52 , THR A:53 , TRP A:54 , ARG A:58 , SER A:63 , PRO A:64 , HIS A:65 , ALA A:226 , PRO A:229 , THR A:262 , GLY A:263 , ARG A:266 , THR A:313 , VAL A:314 , ARG D:51BINDING SITE FOR RESIDUE HEM A 602
7AC7SOFTWARELYS C:119 , ASN C:149 , VAL C:255 , GLY C:256 , THR C:257 , GLY C:258 , GLY C:259 , THR C:260 , ILE C:306 , SER C:349 , PRO C:375 , ASP C:376 , TYR C:381BINDING SITE FOR RESIDUE PLP C 601
8AC8SOFTWAREPRO C:49 , SER C:50 , ARG C:51 , CYS C:52 , THR C:53 , TRP C:54 , SER C:63 , PRO C:64 , HIS C:65 , ARG C:224 , ALA C:226 , PRO C:229 , TYR C:233 , GLY C:263 , ARG C:266 , VAL C:314BINDING SITE FOR RESIDUE HEM C 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L27)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu B:289 -Pro B:290
2Glu D:289 -Pro D:290
3Glu A:289 -Pro A:290
4Glu C:289 -Pro C:290

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L27)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L27)

(-) Exons   (0, 0)

(no "Exon" information available for 4L27)

(-) 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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................ee.hhhhhh....eee..hhhhhh....eeeeee........hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee..........hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.......eeeeee..hhhhhh....hhhhhhhh.........hhhhh.hhhhhh..........hhhhhhhhhhh..eeee.....eeeehhhhhhhhhh................eee....hhhhhhhhh.....eeee.....eeeeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l27 A  41 PLWIRPDAPSRCTWQLGRSESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEEKKPWWWHLRVQELGLSAPLTVLITCGTIEILREKGFNQAPVVDEILGMVTLGNMLSSLLAGKVQPSDVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHERQMVFGVVTAIDLLNFVAAQERD 549
                                    50       |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       405       415       425||  || 438       448  ||   461       471     ||482       492       502       512 ||    534       544     
                                            58|                                                                                                                                                                                                                                                                                                                                                400|                   426|  ||              451|                   477|                                514|                      
                                             61                                                                                                                                                                                                                                                                                                                                                 404                    429  ||               455                    479                                 527                      
                                                                                                                                                                                                                                                                                                                                                                                                                          432|                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                           434                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................hhhhhh....eee..hhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh....................hhhhh.eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......eeeeee..hhhhhh....hhhhhhhh..........hhhhh.hhhhhh...........hhhhhhhhhhhhh..eeeee....eeeeeehhhhhhhhhh.......hhhhh.....eee....hhhhhhhhh.....eeee...eeeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l27 B  42 LWIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFNQAPVVDEGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHEMVFGVVTAIDLLNFVAAQER 548
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401|      413       423       433       443       454       464       474       484       494       504       514|      538       548
                                                                                                                                                                                                                                                                                                                                                                                                 401|                                            451|                                                          514|                   
                                                                                                                                                                                                                                                                                                                                                                                                  404                                             453                                                           529                   


Chain C from PDB  Type:PROTEIN  Length:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................ee.hhhhhh....eee..hhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......eeeeee..hhhhhh....hhhhhhhh........hhhhh.hhhhhh...........hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.......hhhhh.....eeee...hhhhhhhhh.....eeeee...eeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l27 C  42 LWIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFNQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHERQMVFGVVTAIDLLNFVAAQER 548
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       405       415       425       435       445       455       465       475       485       495       505       527       537       547 
                                                                                                                                                                                                                                                                                                                                                                                               399|                                                                                                           514|                     
                                                                                                                                                                                                                                                                                                                                                                                                404                                                                                                            527                     


Chain D from PDB  Type:PROTEIN  Length:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................ee.hhhhhh....eee..hhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhh..eeeee..........hhhhhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......eeeeee..hhhhhh....hhhhhhhh.....hhhhhhhhhhh.hhhhhh...........hhhhhhhhhhhhh..eeee.......eeeehhhhhhhhhh.......hhhhh.....eee....hhhhhhhhhhhh..eeeee..eeeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l27 D  43 WIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFNQAPVVEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHEQMVFGVVTAIDLLNFVAAQER 548
                                    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       403       413       423       433       443     ||454       464       474       484       494       504       514|      537       547 
                                                                                                                                                                                                                                                                                                                                                                                                401|                                           449|                                                            514|                    
                                                                                                                                                                                                                                                                                                                                                                                                 403                                            451                                                             528
   Legend:   → Mismatch (orange background)
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  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 4L27)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L27)

(-) Gene Ontology  (35, 35)

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  4l27
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  4.2.1.22
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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 4l28 4l3v 4pcu 4uuu 5mms

(-) Related Entries Specified in the PDB File

1jbq 4l0d 4l28 4l3v