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(-) Description

Title :  STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE-LIKE PROTEIN HI0607
 
Authors :  S. Korolev, O. Koroleva, T. Zarembinski, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  20 Jan 03  (Deposition) - 29 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Singh, S. Korolev, O. Koroleva, T. Zarembinski, F. Collart, A. Joachimiak, D. Christendat
Crystal Structure Of A Novel Shikimate Dehydrogenase From Haemophilus Influenzae.
J. Biol. Chem. V. 280 17101 2005
PubMed-ID: 15735308  |  Reference-DOI: 10.1074/JBC.M412753200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL SHIKIMATE 5-DEHYDROGENASE-LIKE PROTEIN HI0607
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHI0607
    Organism ScientificHAEMOPHILUS INFLUENZAE
    Organism Taxid727

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ACE3Mod. Amino AcidACETYL GROUP
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ACE-1Mod. Amino AcidACETYL GROUP
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:78 , SER B:80 , HOH B:2150 , HOH B:2192BINDING SITE FOR RESIDUE ACE B 2001
2AC2SOFTWARESER D:11 , GLY D:20 , TYR D:37 , HOH D:2005 , HOH D:2099BINDING SITE FOR RESIDUE ACE D 2002
3AC3SOFTWAREARG C:58 , VAL C:91 , ASP C:93 , HOH C:2005 , HOH C:2052BINDING SITE FOR RESIDUE ACE C 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NPY)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Met A:64 -Pro A:65
2Met A:215 -Pro A:216
3Met B:64 -Pro B:65
4Met B:215 -Pro B:216
5Met C:64 -Pro C:65
6Met C:215 -Pro C:216
7Met D:64 -Pro D:65
8Met D:215 -Pro D:216

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NPY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NPY)

(-) Exons   (0, 0)

(no "Exon" information available for 1NPY)

(-) 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:269
 aligned with Y607_HAEIN | P44774 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         
          Y607_HAEIN      1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFART  269
               SCOP domains d1npya2 A:1-102 Shikimate 5-dehydrogenase-like protein HI0607                                         d1npya1 A:103-269 Shikimate 5-dehydrogenase-like protein HI0607                                                                                                         SCOP domains
               CATH domains 1npyA01 A:1-100 Leucine Dehydrogenase, chain A, domain 1                                            1npyA02 A:101-269 NAD(P)-binding Rossmann-like Domain                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh..eeee.......hhhhh.eehhhhhh.....eeeee..eeeeehhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.eee.........eeee.................hhhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npy A    1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFART  269
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260         

Chain B from PDB  Type:PROTEIN  Length:271
 aligned with Y607_HAEIN | P44774 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
          Y607_HAEIN      1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKF  271
               SCOP domains d1npyb2 B:1-102 Shikimate 5-dehydrogenase-like protein HI0607                                         d1npyb1 B:103-270 Shikimate 5-dehydrogenase-like protein HI0607                                                                                                         - SCOP domains
               CATH domains 1npyB01 B:1-100 Leucine Dehydrogenase, chain A, domain 1                                            1npyB02 B:101-269 NAD(P)-binding Rossmann-like Domain                                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.......hhhhh.eehhhhhh.....eeeee..eeeeehhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.eee.........eeee.................hhhhhhh..eeee.......hhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npy B    1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKx 2001
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|
                                                                                                                                                                                                                                                                                                       270|
                                                                                                                                                                                                                                                                                                       2001-ACE

Chain C from PDB  Type:PROTEIN  Length:271
 aligned with Y607_HAEIN | P44774 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
          Y607_HAEIN      1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKF  271
               SCOP domains d1npyc2 C:1-102 Shikimate 5-dehydrogenase-like protein HI0607                                         d1npyc1 C:103-270 Shikimate 5-dehydrogenase-like protein HI0607                                                                                                         - SCOP domains
               CATH domains 1npyC01 C:1-100 Leucine Dehydrogenase, chain A, domain 1                                            1npyC02 C:101-269 NAD(P)-binding Rossmann-like Domain                                                                                                                    -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh...eeee.......hhhhh.eehhhhhh.....eeeee..eeeeehhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh....eeee..hhhhhhhhhhhh..eee.........eeee.................hhhhhhhh.eeee.......hhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npy C    1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKx 2003
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|
                                                                                                                                                                                                                                                                                                       270|
                                                                                                                                                                                                                                                                                                       2003-ACE

Chain D from PDB  Type:PROTEIN  Length:271
 aligned with Y607_HAEIN | P44774 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:271
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 
          Y607_HAEIN      1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKF  271
               SCOP domains d1npyd2 D:1-102 Shikimate 5-dehydrogenase-like protein HI0607                                         d1npyd1 D:103-270 Shikimate 5-dehydrogenase-like protein HI0607                                                                                                         - SCOP domains
               CATH domains 1npyD01 D:1-100 Leucine Dehydrogenase, chain A, domain 1                                            1npyD02 D:101-269 NAD(P)-binding Rossmann-like Domain                                                                                                                    -- CATH domains
           Pfam domains (1) -----------------Shikimate_dh_N-1npyD05 D:18-90                                           ------------------Shikimate_DH-1npyD01 D:109-222                                                                                    ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------Shikimate_dh_N-1npyD06 D:18-90                                           ------------------Shikimate_DH-1npyD02 D:109-222                                                                                    ------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------Shikimate_dh_N-1npyD07 D:18-90                                           ------------------Shikimate_DH-1npyD03 D:109-222                                                                                    ------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------Shikimate_dh_N-1npyD08 D:18-90                                           ------------------Shikimate_DH-1npyD04 D:109-222                                                                                    ------------------------------------------------- Pfam domains (4)
         Sec.struct. author ......eeeeee.....hhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh..eeee.......hhhhh.eehhhhhh.....eeeee..eeeeehhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh....eeee..hhhhhhhhhhhhh.eee.........eeee.................hhhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1npy D    1 MINKDTQLCMSLSGRPSNFGTTFHNYLYDKLGLNFIYKAFTTQDIEHAIKGVRALGIRGCAVSMPFKETCMPFLDEIHPSAQAIESVNTIVNDNGFLRAYNTDYIAIVKLIEKYHLNKNAKVIVHGSGGMAKAVVAAFKNSGFEKLKIYARNVKTGQYLAALYGYAYINSLENQQADILVNVTSIGMKGGKEEMDLAFPKAFIDNASVAFDVVAMPVETPFIRYAQARGKQTISGAAVIVLQAVEQFELYTHQRPSDELIAEAAAFARTKx 2002
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270|
                                                                                                                                                                                                                                                                                                       270|
                                                                                                                                                                                                                                                                                                       2002-ACE

   Legend:   → Mismatch (orange background)
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    → 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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (2, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 8)

Asymmetric Unit

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Y607_HAEIN | P44774)
molecular function
    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:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
biological process
    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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