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(-) Description

Title :  STRUCTURAL INSIGHTS INTO SUBSTRATE AND COFACTOR SELECTION BY SP2771
 
Authors :  Y. A. Yuan, Z. Yuan, B. Yin, D. Wei
Date :  09 Oct 12  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Substrate Selection, Cofactor Preference, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yuan, B. Yin, D. Wei, Y. A. Yuan
Structural Basis For Cofactor And Substrate Selection By Cyanobacterium Succinic Semialdehyde Dehydrogenase
J. Struct. Biol. V. 182 125 2013
PubMed-ID: 23500184  |  Reference-DOI: 10.1016/J.JSB.2013.03.001

(-) Compounds

Molecule 1 - SUCCINATE-SEMIALDEHYDE DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SYNPCC7002_A2771
    Mutation: YES
    Organism Scientific: SYNECHOCOCCUS
    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, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2SSN2Ligand/Ion4-OXOBUTANOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:131 , PHE A:132 , TRP A:135 , GLN A:136 , ARG A:139 , SER A:261 , ALA A:262 , SER A:419 , NAP A:502 , HOH A:744 , HOH A:759 , HOH A:767BINDING SITE FOR RESIDUE SSN A 501
2AC2SOFTWAREVAL A:127 , MET A:128 , TRP A:130 , ASN A:131 , GLN A:136 , ARG A:139 , LYS A:154 , HIS A:155 , ALA A:156 , SER A:157 , ALA A:187 , THR A:205 , GLY A:206 , SER A:207 , ALA A:210 , GLU A:228 , LEU A:229 , GLY A:230 , ALA A:262 , GLU A:359 , PHE A:361 , LEU A:387 , PHE A:425 , SSN A:501 , HOH A:626 , HOH A:640 , HOH A:686 , HOH A:863 , HOH A:873 , HOH A:891 , HOH A:901 , HOH A:917 , HOH A:1098 , HOH A:1163 , HOH A:1164BINDING SITE FOR RESIDUE NAP A 502
3AC3SOFTWAREASN B:131 , PHE B:132 , TRP B:135 , GLN B:136 , ARG B:139 , SER B:261 , ALA B:262 , SER B:419 , NAP B:502 , HOH B:763 , HOH B:783 , HOH B:966BINDING SITE FOR RESIDUE SSN B 501
4AC4SOFTWAREVAL B:127 , MET B:128 , TRP B:130 , ASN B:131 , GLN B:136 , ARG B:139 , LYS B:154 , HIS B:155 , ALA B:156 , SER B:157 , ALA B:187 , VAL B:190 , THR B:205 , GLY B:206 , SER B:207 , ALA B:210 , GLU B:228 , LEU B:229 , GLY B:230 , ALA B:262 , GLU B:359 , PHE B:361 , LEU B:387 , PHE B:425 , SSN B:501 , HOH B:669 , HOH B:680 , HOH B:687 , HOH B:879 , HOH B:893 , HOH B:905 , HOH B:1075 , HOH B:1076 , HOH B:1135BINDING SITE FOR RESIDUE NAP B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VZ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VZ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VZ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VZ3)

(-) Exons   (0, 0)

(no "Exon" information available for 3VZ3)

(-) 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
 aligned with B1XMM6_SYNP2 | B1XMM6 from UniProtKB/TrEMBL  Length:454

    Alignment length:453
                                    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   
         B1XMM6_SYNP2     2 AIATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 454
               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.....eeee....hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.eeee..............eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vz3 A   2 AIATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSAIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 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
 aligned with B1XMM6_SYNP2 | B1XMM6 from UniProtKB/TrEMBL  Length:454

    Alignment length:453
                                    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   
         B1XMM6_SYNP2     2 AIATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 454
               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.....eeee....hhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh.eeee..............eeee.....hhhhhh.....eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee..............hhh.ee...hhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vz3 B   2 AIATINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSKFAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANEYTETQATESYVCYQPLGILLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTLLIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADLDEAVEVGTVARTMNNGQSAIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGPLATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAPVAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRLPFGGTKRSGYGRELGLAGIRTFVNAKTVWLK 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)
  - → 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 3VZ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VZ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VZ3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B1XMM6_SYNP2 | B1XMM6)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/TrEMBL
        B1XMM6_SYNP2 | B1XMM6: 3vz1 3vz2 4it9 4ita 4itb

(-) Related Entries Specified in the PDB File

3vz0 3vz1 3vz2