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(-) Description

Title :  STRUCTURE OF BACTERIAL ENZYME IN COMPLEX WITH COFACTOR AND SUBSTRATE
 
Authors :  S. Rhee, J. Park
Date :  18 Jan 13  (Deposition) - 24 Apr 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Oxidoreductase, Oxidoreductase-Substrate Complex (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  (3, 28)

Asymmetric/Biological Unit (3, 28)
No.NameCountTypeFull Name
1EDO24Ligand/Ion1,2-ETHANEDIOL
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3SSN2Ligand/Ion4-OXOBUTANOIC ACID

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:127 , MET A:128 , PRO A:129 , TRP A:130 , ASN A:131 , GLN A:136 , LYS A:154 , HIS A:155 , ALA A:156 , SER A:157 , ALA A:187 , GLY A:206 , SER A:207 , ALA A:210 , SER A:213 , GLU A:228 , LEU A:229 , ILE A:309 , GLU A:359 , PHE A:361 , SSN A:502 , EDO A:506 , HOH A:625 , HOH A:715 , HOH A:738 , HOH A:782 , HOH A:925BINDING SITE FOR RESIDUE NDP A 501
02AC2SOFTWAREASN A:131 , TRP A:135 , ARG A:139 , GLU A:228 , CYS A:262 , SER A:419 , NDP A:501 , HOH A:647 , HOH A:649 , HOH A:775BINDING SITE FOR RESIDUE SSN A 502
03AC3SOFTWAREGLU A:167 , GLU A:171 , PHE A:175 , PRO A:176 , VAL A:179 , PHE A:180 , HOH A:607 , HOH A:616 , HOH A:653BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWARELEU 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:730BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREPRO A:22 , ARG A:48 , GLU A:96 , SER A:188 , GLN A:189 , HOH A:670BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREASP A:312 , GLN A:316 , GLU A:359 , LEU A:360 , PHE A:361 , NDP A:501BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREGLU A:34 , ALA A:35 , GLU A:177 , HOH A:634 , SER B:45BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREPRO A:224 , THR A:225 , EDO A:509 , PRO B:224 , THR B:225 , TYR B:433 , HOH B:769BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREALA A:215 , GLY A:219 , LYS A:223 , THR A:225 , TYR A:433 , EDO A:508 , GLY B:219 , TYR B:433BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREGLU A:208 , LEU A:229 , GLY A:230 , GLU A:359 , HOH A:704BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREPRO A:22 , GLU A:99 , GLN A:100 , GLN A:192 , HOH A:608 , HOH A:700BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWARETYR A:106 , GLU A:108 , GLN A:220 , HOH A:803BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWAREGLY A:409 , ALA A:410 , PRO A:424 , PHE A:425 , GLY A:426 , ARG A:435 , HOH A:748 , ALA B:448 , THR B:450BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREASP A:407 , THR A:428 , LYS A:429 , HOH A:742 , LEU B:121 , ASN B:447 , HOH B:651BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWAREILE A:3 , LYS A:154 , HIS A:155 , ALA A:156 , SER A:157 , PRO A:160 , LEU A:183 , LEU A:184 , ILE A:185 , HOH A:606BINDING SITE FOR RESIDUE EDO A 515
16BC7SOFTWAREVAL B:127 , MET B:128 , PRO B:129 , TRP B:130 , ASN B:131 , LYS B:154 , HIS B:155 , ALA B:156 , SER B:157 , ALA B:187 , GLY B:206 , SER B:207 , ALA B:210 , SER B:213 , GLU B:228 , GLY B:230 , ILE B:309 , GLU B:359 , PHE B:361 , SSN B:502 , HOH B:650 , HOH B:723 , HOH B:751 , HOH B:854 , HOH B:938 , HOH B:941 , HOH B:945BINDING SITE FOR RESIDUE NDP B 501
17BC8SOFTWAREASN B:131 , TRP B:135 , GLN B:136 , ARG B:139 , GLU B:228 , CYS B:262 , SER B:419 , NDP B:501 , HOH B:631 , HOH B:647 , HOH B:759BINDING SITE FOR RESIDUE SSN B 502
18BC9SOFTWAREGLU B:167 , GLU B:171 , PHE B:175 , PRO B:176 , VAL B:179 , PHE B:180 , HOH B:612 , HOH B:615 , HOH B:683BINDING SITE FOR RESIDUE EDO B 503
19CC1SOFTWAREPRO B:22 , ARG B:48 , GLU B:99 , GLN B:100 , GLN B:192 , HOH B:605 , HOH B:691 , HOH B:727BINDING SITE FOR RESIDUE EDO B 504
20CC2SOFTWARESER B:288 , LEU B:289 , ASP B:300 , HOH B:696 , HOH B:762 , HOH B:907BINDING SITE FOR RESIDUE EDO B 505
21CC3SOFTWAREPRO B:22 , ARG B:48 , GLU B:96 , SER B:188 , GLN B:189 , HOH B:691BINDING SITE FOR RESIDUE EDO B 506
22CC4SOFTWARELEU A:121 , ASN A:447 , HOH A:667 , ASP B:407 , THR B:428 , LYS B:429 , HOH B:734BINDING SITE FOR RESIDUE EDO B 507
23CC5SOFTWARELEU 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:754BINDING SITE FOR RESIDUE EDO B 508
24CC6SOFTWAREARG B:40 , ARG B:47 , TYR B:118 , PRO B:120 , ALA B:147BINDING SITE FOR RESIDUE EDO B 509
25CC7SOFTWAREGLU B:208 , LEU B:229 , GLU B:359 , HOH B:705BINDING SITE FOR RESIDUE EDO B 510
26CC8SOFTWAREHOH B:887 , HOH B:900BINDING SITE FOR RESIDUE EDO B 511
27CC9SOFTWARETYR B:106 , GLU B:108 , GLN B:220 , HOH B:774BINDING SITE FOR RESIDUE EDO B 512
28DC1SOFTWAREALA A:448 , THR A:450 , GLY B:409 , ALA B:410 , PRO B:424 , PHE B:425 , GLY B:426 , ARG B:435 , HOH B:715BINDING SITE FOR RESIDUE EDO B 513

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ITB)

(-) 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:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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
                 4itb A   2 AIATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 454
                                    11        21        31        41        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       411       421       431       441       451   


Chain B from PDB  Type:PROTEIN  Length:453
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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....eeeeeee..hhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.eeee..............eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4itb B   2 AIATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 454
                                    11        21        31        41        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       411       421       431       441       451
   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 4ITB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        B1XMM6_SYNP2 | B1XMM6: 3vz1 3vz2 3vz3 4it9 4ita

(-) Related Entries Specified in the PDB File

4it9 4ita