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(-) Description

Title :  STRUCTURE OF BACTERIAL ENZYME
 
Authors :  S. Rhee, J. Park
Date :  18 Jan 13  (Deposition) - 24 Apr 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Park, S. Rhee
Structural Basis For A Cofactor-Dependent Oxidation Protection And Catalysis Of Cyanobacterial Succinic Semialdehyde Dehydrogenase.
J. Biol. Chem. V. 288 15760 2013
PubMed-ID: 23589281  |  Reference-DOI: 10.1074/JBC.M113.460428

(-) Compounds

Molecule 1 - SUCCINATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SYNECHOCOCCUS SP.
    Organism Taxid: 32049
    Strain: ATCC 27264 / PCC 7002 / PR-6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 33)

Asymmetric/Biological Unit (2, 33)
No.NameCountTypeFull Name
1EDO31Ligand/Ion1,2-ETHANEDIOL
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:224 , THR A:225 , TYR A:433 , HOH A:835 , PRO B:224 , THR B:225 , TYR B:433BINDING SITE FOR RESIDUE EDO A 501
02AC2SOFTWAREGLY A:409 , ALA A:410 , PRO A:424 , PHE A:425 , GLY A:426 , ARG A:435 , ALA B:448 , THR B:450BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREGLU A:167 , GLU A:171 , PHE A:175 , PRO A:176 , VAL A:179 , PHE A:180 , HOH A:616 , HOH A:622 , HOH A:706BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREASP A:312 , GLN A:316 , GLU A:359 , LEU A:360 , PHE A:361 , EDO A:509 , HOH A:866BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREGLU A:99 , GLN A:100 , GLN A:192 , HOH A:623 , HOH A:885BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREPRO A:22 , ARG A:48 , GLU A:96 , SER A:188 , GLN A:189 , HOH A:757BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREGLU A:208 , LEU A:229 , GLY A:230 , GLU A:359 , HOH A:653BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWARELEU A:124 , PRO A:143 , ALA A:144 , ASN A:149 , GLY A:441 , ILE A:442 , THR A:444 , PHE A:445 , HOH A:671BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREGLU A:359 , PHE A:361 , EDO A:504 , HOH A:866BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREMET A:256 , SER A:261 , ILE A:263 , MET A:416BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREHIS A:155 , ALA A:156 , ALA A:163 , LEU A:183 , LEU A:184 , ILE A:185BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREGLN A:319 , ALA A:320 , LYS A:354 , ILE A:355 , HOH A:677BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWAREARG A:267 , LEU A:356 , GLN A:357 , LEU A:379 , ASP A:382BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREPHE A:44 , ARG A:47 , LEU A:102 , TYR A:118 , PRO A:120 , ALA A:147 , EDO A:515 , EDO A:516BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWAREARG A:40 , PRO A:120 , EDO A:514BINDING SITE FOR RESIDUE EDO A 515
16BC7SOFTWARETHR A:42 , PHE A:44 , ARG A:47 , EDO A:514 , HOH A:678BINDING SITE FOR RESIDUE EDO A 516
17BC8SOFTWAREALA A:187 , VAL A:190 , ALA A:210 , SER A:213 , LEU A:214BINDING SITE FOR RESIDUE EDO A 517
18BC9SOFTWARELYS A:154 , ALA A:156 , SER A:157 , ALA A:187 , HOH A:693BINDING SITE FOR RESIDUE PO4 A 518
19CC1SOFTWARESER A:45 , GLU B:34 , ALA B:35 , HOH B:680BINDING SITE FOR RESIDUE EDO B 501
20CC2SOFTWAREGLU B:167 , GLU B:171 , PHE B:175 , PRO B:176 , VAL B:179 , PHE B:180 , HOH B:626 , HOH B:632 , HOH B:746BINDING SITE FOR RESIDUE EDO B 502
21CC3SOFTWAREGLU B:99 , GLN B:100 , GLN B:192 , HOH B:614 , HOH B:888BINDING SITE FOR RESIDUE EDO B 503
22CC4SOFTWAREGLN B:316 , GLU B:359 , LEU B:360 , PHE B:361 , EDO B:510 , HOH B:851BINDING SITE FOR RESIDUE EDO B 504
23CC5SOFTWAREILE A:57 , ALA A:172 , HOH A:759 , ILE B:57 , ALA B:172 , HOH B:712BINDING SITE FOR RESIDUE EDO B 505
24CC6SOFTWAREPHE B:132 , MET B:256 , SER B:261 , ILE B:263 , MET B:416 , EDO B:511BINDING SITE FOR RESIDUE EDO B 506
25CC7SOFTWAREPRO B:22 , ARG B:48 , GLU B:96 , SER B:188 , GLN B:189 , HOH B:803BINDING SITE FOR RESIDUE EDO B 507
26CC8SOFTWAREGLU B:208 , LEU B:229 , GLY B:230 , GLU B:359 , HOH B:640BINDING SITE FOR RESIDUE EDO B 508
27CC9SOFTWARELEU B:124 , PRO B:143 , ALA B:144 , ASN B:149 , GLY B:441 , ILE B:442 , THR B:444 , PHE B:445 , HOH B:701BINDING SITE FOR RESIDUE EDO B 509
28DC1SOFTWAREILE B:309 , GLU B:359 , PHE B:361 , EDO B:504 , HOH B:851BINDING SITE FOR RESIDUE EDO B 510
29DC2SOFTWARETRP B:135 , GLN B:136 , CYS B:262 , SER B:419 , EDO B:506 , HOH B:644BINDING SITE FOR RESIDUE EDO B 511
30DC3SOFTWARESER B:288 , LEU B:289 , ASP B:300 , HOH B:707 , HOH B:742 , HOH B:880BINDING SITE FOR RESIDUE EDO B 512
31DC4SOFTWAREGLN B:319 , ALA B:320 , ALA B:353 , LYS B:354 , ILE B:355 , HOH B:714BINDING SITE FOR RESIDUE EDO B 513
32DC5SOFTWAREALA B:187 , ALA B:210 , SER B:213 , LEU B:214 , HOH B:885BINDING SITE FOR RESIDUE EDO B 514
33DC6SOFTWARELYS B:154 , ALA B:156 , SER B:157 , ALA B:187 , HOH B:730 , HOH B:885BINDING SITE FOR RESIDUE PO4 B 515

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IT9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IT9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IT9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IT9)

(-) Exons   (0, 0)

(no "Exon" information available for 4IT9)

(-) 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:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhh...eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.eeee..............eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4it9 A   3 IATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 454
                                    12        22        32        42        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       402       412       422       432       442       452  


Chain B from PDB  Type:PROTEIN  Length:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......eeee....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhh...eeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.eeee..............eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4it9 B   3 IATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 454
                                    12        22        32        42        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       402       412       422       432       442       452
   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 4IT9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IT9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IT9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        B1XMM6_SYNP2 | B1XMM6: 3vz1 3vz2 3vz3 4ita 4itb

(-) Related Entries Specified in the PDB File

4ita 4itb