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(-) Description

Title :  CRYSTAL STRUCTURE OF DELTA516-525 HUMAN CYSTATHIONINE BETA-SYNTHASE
 
Authors :  J. Ereno, T. Majtan, I. Oyenarte, J. P. Kraus, L. A. Martinez
Date :  07 Jun 13  (Deposition) - 18 Sep 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.63
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B  (2x)
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, 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
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BETA-THIONASE, SERINE SULFHYDRASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x):  B 
Biological Unit 2 (1x): A C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2PLP3Ligand/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  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:119 , ASN B:149 , SER B:254 , VAL B:255 , GLY B:256 , THR B:257 , GLY B:258 , GLY B:259 , THR B:260 , GLY B:305 , ILE B:306 , SER B:349 , PRO B:375 , ASP B:376 , TYR B:381BINDING SITE FOR RESIDUE PLP B 601
2AC2SOFTWARETHR A:53 , ARG A:58 , HEM A:602 , SER B:50 , ARG B:51 , CYS B:52 , THR B:53 , TRP B:54 , ARG B:58 , 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 , ARG B:266 , THR B:313BINDING SITE FOR RESIDUE HEM B 602
3AC3SOFTWARELYS 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 , GLY A:305 , ILE A:306 , SER A:349 , PRO A:375 , ASP A:376BINDING SITE FOR RESIDUE PLP A 601
4AC4SOFTWARESER A:50 , ARG A:51 , CYS A:52 , THR A:53 , TRP A:54 , ARG A:58 , PRO A:59 , GLU A:62 , SER A:63 , PRO A:64 , HIS A:65 , ALA A:226 , LEU A:230 , TYR A:233 , GLY A:263 , ARG A:266 , VAL A:314 , THR B:53 , ARG B:58 , HEM B:602BINDING SITE FOR RESIDUE HEM A 602
5AC5SOFTWARELYS C:119 , ASN C:149 , SER C:254 , VAL C:255 , GLY C:256 , THR C:257 , GLY C:258 , GLY C:259 , THR C:260 , GLY C:305 , ILE C:306 , SER C:349 , PRO C:375 , ASP C:376 , TYR C:381BINDING SITE FOR RESIDUE PLP C 601
6AC6SOFTWAREPRO C:49 , ARG C:51 , CYS C:52 , THR C:53 , TRP C:54 , PRO C:59 , GLU C:62 , SER C:63 , PRO C:64 , HIS C:65 , ARG C:224 , ALA C:226 , LEU C:230 , 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 4L3V)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L3V)

(-) Exons   (0, 0)

(no "Exon" information available for 4L3V)

(-) 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhh............ee.hhhhhh....eee.hhhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhh....hhhhhhhh...hhhhhhhhhhhhhh.hhhhhh...........hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.......hhhhhh....eee....hhhhhhhhh.....eeee.....eeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l3v A  41 PLWIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDLTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHERQMVFGVVTAIDLLNFVAAQERDQ 550
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510   ||  532       542        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   514|                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    527                       


Chain B from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhh...............hhhhhh....eee..hhhhhh....eeeeee.hhh....hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhh.eeeee..........hhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhh...eeeeeee.......hhhhhh..........................eeeeehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhh....hhhhhhhh...hhhhhhhhhhhhhh.hhhhhh...........hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.......hhhhhh....eee....hhhhhhhhhh....eeee.....eeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l3v B  41 PLWIRPDAPSRCTWQLGRPASESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDLTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHERQMVFGVVTAIDLLNFVAAQERDQ 550
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510   ||  532       542        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   514|                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    527                       


Chain C from PDB  Type:PROTEIN  Length:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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...hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhh....hhhhhhhh...hhhhhhhhhhhhhh.hhhhhh...........hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.......hhhhhh....eee....hhhhhhhhhh....eeee.....eeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l3v C  41 PLWIRPDAPSRCTWQLGRPSESPHHHTAPAKSPKILPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTLKPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNARFDSPESHVGVAWRLKNEIPNSHILDQYRNASNPLAHYDTTADEILQQCDGKLDMLVASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSILAEPEELNQTEQTTYEVEGIGYDFIPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRCVVILPDSVRNYMTKFLSDRWMLQKGFLKEEDLTEKKPWWWHLRVQELGLSAPLTVLPTITCGHTIEILREKGFDQAPVVDEAGVILGMVTLGNMLSSLLAGKVQPSDQVGKVIYKQFKQIRLTDTLGRLSHILEMDHFALVVHERQMVFGVVTAIDLLNFVAAQERDQ 550
                                    50        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       411       421       431       441       451       461       471       481       491       501       511  ||   533       543       
                                             59|                                                                                                                                                                                                                                                                                                                                                                                                                                                                  514|                       
                                              61                                                                                                                                                                                                                                                                                                                                                                                                                                                                   527
   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 4L3V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L3V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L3V)

(-) Gene Ontology  (35, 35)

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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 4pcu 4uuu 5mms

(-) Related Entries Specified in the PDB File

1jbq 4l0d 4l27 4l28